All Classes and Interfaces
Class
Description
A special
ImageMetadataReader that will always throw an exception and reject a file.Copies files to a number
001, 002 etc.Names of the channels from the metadata if it exists, or after RGB, or by index.
The headers found in a BMP file.
Uses different raster-writers depending on the number/type of channels.
If the extension(s) of a path matches a particular value, then use a particular reader, otherwise
a fallback.
Uses one input-manager normally, but a different one if in debug mode.
Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly
3D.
Selects particular writers based on if particular suggested image formats are present.
Makes a simple bytewise copy of a file, where no byte is changed.
Associates particular timestamp with each file, and clusters.
Uniquely identifies a cluster.
A mapping of files to membership of particular clusters.
Removes the file-name from a path, but keeps the directories and preserves the file-extension.
Combines multiple CSV files into a single CSV file.
Create a voxelwise compressed copy of any TIFF file being copied, and otherwise do a
Bytewise copy.Concatenates the inputs from multiple
InputManagers that all provide the same input-type.Always generates a constant path irrespective of the the input
An input object that converts
NamedChannelsInput to StackSequenceInput.Manager that converts (one channel)
NamedChannelsInput to StackSequenceInput.Context parameters when copying many files from a source directory to a destination directory.
Copy files to the output-directory, possibly changing the name or performing other operations
like compression in the process.
A method used for copying files (e.g.
How an output name (and path) is selected for an input file when copying.
Base class for implementations of
CopyFilesNaming where each file is copied independently
of the others.How to style a date in a file-name.
Lists all directories to a certain depth
Reuses the directories between a path and its root to form the output - and also the filename.
Excludes all inputs whose identifiers match a regular expression.
Remembers each unique extension, and associated count
Extracts the identifier from an
InputFromManager to summarize further.Extracts the identifier and path from an
InputFromManager to summarize further.Extracts a
Path from an input to summarize further.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.
Tracks the range of file-size.
Finds a CSV file with the names of an input as the first-column.
Filters all the input objects for only those with certain types of descriptive-names.
Filters a list of input-objects by the descriptive name.
Filters a list of inputs when in debug-mode
Rejects files that fail to match a particular regular-expression
Combines all series and frames returned by a reader by converting them into multiple channels in
the same image.
Counts the frequency of certain strings, and describes the contents in human language.
The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create
an output prefix.
An
InputManagerWithStackReader that can unify separate images in separate files to form a
single Stack.Populates
ImageMetadata from the header of an image-file.When a
IndexRangeNegative is passed as an argument, an InputGrouper is
constructed that extracts elements from a Path.Multiplexes between two
PathPrefixers depending on whether an incrementing number
sequence was output was requested.Multiplexes between two namers depending on if the relative-to-directory option is
selected.
Summarizes the size of images.
Adds an explicit
Resolution to an image after it has been read.Tries to construct the
ImageMetadata from EXIF and other metadata, if available, or
otherwise falls back to another reader.Generates an out string where $digit$ is replaced with the #digit group from a regex
Generates an outstring of the form
The headers found in a JPEG file.
Derives a name by taking the filename together with optionally several subdirectories names.
Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
Limits the number of input-objects to a certain hard-maximum
Like
Limit if it is requested in the InputContextParameters, makes no change to
the inputs.An image viewed as a set of channels, each with a unique name.
Parent for all the
NamedChannels classesImplementation of
NamedFilesBase that is an InputManager that accepts FileInput as input and derives a name.Base class for an
InputManager that produces inputs that are created from a NamedFile.Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
Converts a number to a strings of constant width by padding with leading zeros.
A
OpenedImageFile where the image is formed from more than one file on the file-system.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.A collection of
FileDetails objects with methods to query their properties.Helper routines for performing operations on
Paths.Matches a regex against incoming file-paths to form a prefix for output
Finds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the
name.
The headers found in a PNG file.
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.
Reads
Resolution from an XML file associated an image.A counter that also records outputs in a message-log and CSV file.
A base class for
CopyFilesNaming classes that use a regular-expression.If the XY resolution of an opened-image meets a certain condition then the resolution is scaled
by a factor.
Constructs a name by finding the relative-path between the file and the input-directory.
Removes extensions from the identifier (but not from the file) and only if the extension
hasn't already been removed upstream.
Splits an identifier into elements by the directory separator, and removes the final element.
Removes any whitespace characters from the path
Generates a file-path by replacing all occurrences of a string-pattern with another
Reads and writes a metadata XML file specifying the image-resolution.
Prepend a 'root' before the file-path-prefix obtained from a delegate
Represents a set of files, with a different path-root depending on context.
A collection of root-paths indexed by their name.
Rotates an image to match any EXIF orientation information, if it exists.
Randomly shuffles the order of the inputs.
Like
Shuffle if requested in the InputContextParameters otherwise makes no change
to the inputs.For an image with a single channel
Remembers the different sizes among the files
Sorts the input-items in alphabetical order of their input-name.
An
InputManager where each file provides one or more
Stacks.A base class for a
StackWriter delegates to another StackWriter based on values
of a StackWriteAttributes.If specified in the context, the existing name if subsetted according to an index range.
A regular expression substitution (replaceAll) is applied to the relative-path
Summarizes a set of elements by outputting a descriptive string.
Collects summary data about a set of input files that will eventually be outputted to the user
A count of the number of inputs.
Summarizes
ImageMetadataInput in different ways.A simple summarizer, where there's one summary-item per image.
Extracts a particular item from an
InputFromManager for further summarization downstream.Creates a string where each line is an element.
Base class for
Summarizers that operate on the Path associated with inputs.Multiplexes between two summarizers depending on the total number of count.
Derives a human-friendly name for a time-interval.
Extracts a timestamp from a file-name if it exists.
How to style a time in a file-name.
When writing a stack, an additional file is written to indicate the physical voxel sizes, if this
information is known.