All Classes and Interfaces
Class
Description
A feature that calculates the absolute value of another feature's result.
The condition is accepted if any one of a list of
AcceptIterationPredicate fulfills the
condition.A condition that must be fulfilled for a particular iteration of a morphological operation to be
accepted.
Provides functions to provide access and creation to/from the object-mask representation of a
generic type.
Provides access to the simple-case of a list of
ObjectMasks.Reads the image acquisition-date. from EXIF metadata, if specified in an image-file.
Adds a constant value to each voxel in a channel.
A feature that adds a constant value to the result of another feature.
Criteria for adding edges between marks in a graph-based model.
Implements
AddCriteria for energy pairs, combining energy calculations with additional
criteria.An implementation of
AddCriteria that never adds an edge between marks.An
AddCriteriaPair that combines multiple criteria using a logical OR operation.Abstract base class for criteria used to determine if a pair of marks should be included.
Adds edge filters and their gradients to a
Define object.Adds options relating to inputting from the command-line.
Base class for adding options from command-line arguments.
Adds options relating to outputting from the command-line.
Adds an individual-item to an aggregate-item.
Adds additional outputs-names to be enabled to the defaults.
A condition to be checked after merging two
ObjectMasks.Aggregates many per-image annotations together in form of a CSV file.
Creates a an aggregated-image for each group, where each voxel-value is aggregated across each
channel in each image in the group.
Align the bounding-box to the
larger without resizing.How the alignment will occur for a particular dimension.
All outputs are allowed irrespective of
outputName.Selects all possible channels from all possible stacks
Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
Creates a new mask of particular dimensionality where all values are off.
Creates a new mask of particular dimensionality where all values are on.
Specifies a single object that will always be the "match" for whatever source object.
Allows every output, irrespective of whether the
OutputterChecked allows the output-name.Always create a new
SessionInputSequential with no reuse or caching between calls.A special
ImageMetadataReader that will always throw an exception and reject a file.The base class of all beans used in Anchor.
Base class for all Anchor-specific bean factories.
A base class for all checked exceptions used on the Anchor platform.
An exception that can be combined with similar exceptions and summarized.
The default bean factory used for initializing
AnchorBeans.A base class for particular checked-exceptions which are guaranteed to provide a user-friendly
error description.
A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly
error description.
A run-time exception to throw in situations which should never logically occur by design.
This is an exception that should never be thrown, but can be used for type-safety where an
exception is needed.
A base class for all unchecked (runtime) exceptions used on the Anchor platform.
A centralized location for hyperlinks to the Anchor website.
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
Applies multiples filter with logical AND i.e. an object must pass all objects in the list to
remain.
Combines two UpdatableBeforeConditions as LOGICAL ANDs
Combines two
BinaryKernels so that they only a true value exists only at a point where
both kernels return true.Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
Performs Perona-Malik Anisotropic
Diffusion.
Base class for types of image annotations.
Generates a CSV file containing aggregated annotation data.
How to display one or more
Stacks as background during an annotation process.Compares similar object-sets produced from two different sources.
Input for annotation comparison, containing sources to compare and associated metadata.
An input manager for annotation comparison that extends
InputManagerWithStackReader.Allows an annotation to be deleted from the file-system.
An
InputManager that provides annotations corresponding to images.Represents a label used for annotation, with associated metadata.
Allows an annotation to be read from the file-system.
An image-annotation that involves a mark-collection.
One particular annotation, associated with its strategy.
Allows an annotation to be written to the file-system.
How an input is associated with annotations on the file-system, and how this is presented
visually.
Copies files to a number
001, 002 etc. in the same order they are inputted.Applies an ImageJ (2D) morphological operation to voxels.
Applies various kinds of
Kernel to BinaryVoxels.Calculates deterministically a point that is definitely inside the object-mask and outputs a
selected axis value.
If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
Area of the stack (XY dimensions only, Z dimension is not considered).
Area expressed in square meters, or units thereof.
Area expressed in pixels.
Converts string passed as arguments.
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
Base class for arithmetic operations that conditionally overwrite voxel values with a constant.
Creates a stack that combines other stacks.
When the position of a particular
RGBStack cannot be determined, when combined with
others onto a single plane.Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask
feature
Allows assignment of parameters if they are are of type
paramTypeMatch or subclass of it.Utilities for assigning a name to a feature.
Copies the pixels from
channelAssignFrom to channel (possibly masking).Assigns a value from a dictionary to all voxels in a channel.
Matches source-objects to target objects, based upon intersection, and assigns the value in the
respective source object to the target object
A one-to-one pairing between items in two respective sets.
Different
ColorSchemes that can be used to select colors for paired and unpaired objects.Outputs a raster showing an
Assignment on a background.Creates a one-to-one assignment between two sets of
ObjectMasks.When the assignment of a permuted value to a property cannot succeed.
Abstract class for assigning priorities to potential object merges.
Allows merges if there is an increase in the payload i.e.
Calculates pair-feature on each potential merge, and this value determines priority..
Assigns a constant (scalar) value to the portion of the image covered by a mask
Extracts one of the memos from the pair, and processes as a
FeatureSingleMemoAssociated an index with the object.
For classes that wish to have a XmlConfiguration associated with them.
Base class for features that check if an object is at the border of an image.
Checks if an object's bounding box is at the border of the image in the XY plane.
Checks if an object's bounding box is at the border of the image in the Z dimension.
Extract a single
ObjectMask into a new collection.Perform a segmentation at a different scale, and then fit the results back to the original scale.
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
Names of the channels from the metadata if it exists, or after RGB, or by index.
Identifies axis in a Cartesian coordinate system.
Creates a
DirectionVector that is a unit-vector along a particular image-axis.When converting another type to a corresponding
Axis fails.Calculates the axis ratio of an
Ellipsoid.Utility class for creating background
DisplayStacks.Subtracts background from a channel using ImageJ's
BackgroundSubtracter.Creates a single
AnchorBean from XML.An exception occurs when the duplication of a bean fails.
Indicates that a field in an Anchor Bean class is
to be treated as a bean-field.
Parent class for all state used to initialise beans in
InitializableBean.Tries to initialize a bean and it's children with particular parameters, if possible.
Maps a
AnchorBean family-type to a bean that belongs to the family.Creates a
BeanInstanceMap with useful entries for testing, and associates it with bean
creation.Like
BeanCreator but creates a list of beans.If a Bean is misconfigured.
A bean's XML is thrown when a bean has misconfigured XML.
Calculates file-system paths involving an
AnchorBean.A provider base-class that as well as providing type
S, also provides a Stack.When something quite strange happens that we don't usually want to catch.
Checks to see if a bean has been misconfigured, when created manually in tests (thereby skipping
the usual checks during the BeanXML loading process).
An exception that occurs when one cannot process BeanXML for some reason.
Creates beans based on XML specifying their properties (including nested children).
A condition to be checked before merging two
ObjectMasks.Tests two arguments of type
float as a predicate.Tests two arguments of type
int as a predicate.Tests two arguments of type
long as a predicate.Labels images using a binary classifier.
Base class for kernels that return a boolean for every voxel.
A parent class for any
BinaryKernel that implements a morphological operation.Selects voxels that are not off voxels.
Selects voxels that are not on voxels.
Selects only the off voxels.
Getters and setters for reading and assigning binary state to voxels.
Selects only the on pixels.
Abstract base class for image labellers that produce binary outcomes (positive or negative).
Performs a segmentation on voxels so that each voxel has an on or off state after
the operation.
Parameters that are passed during a
BinarySegmentation.Uses an existing
BinarySegmentation that is located by a unique identifier.Implementation of
BinarySegmentation that performs global
thresholding.An implementation of
BinarySegmentation that delegates to one other BinarySegmentation.Performs a binary-segmentation using the upstream objects as masks.
Two values representing
byte binary states in an UnsignedByteBuffer.Two values representing
int binary states in an unsigned-byte buffer.Like
Voxels but should only contain two distinct intensity-values representing on
and off. states.A base class for implementations of
RelationToThreshold where the threshold is derived
from a BinaryValuesInt.Creates
BinaryVoxels parameterized by size and initial state.When an outputter cannot be successfully bound to an output directory.
Reads a stack using the Bioformats
library.
Base class for writing a stack to the filesystem using the Bioformats library.
Tests two arguments of type
short as a predicate.The bit-depth of the image per channel.
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
Performs a Gaussian Blur in 3D
Performs a Gaussian-blur in 2D on each slice independently
A method for applying blurring to an image.
The headers found in a BMP file.
An abstract class representing an upper and lower bound.
Represents an upper and lower bound in degrees which is converted to radians when resolved.
One or more elements, each with an individual bounding-box, and collectively with a bounding-box
that fully contains them all.
Voxels that exist within a particular bounding-box in an image.A bounding-box in two or three dimensions.
Base class for features that calculate a value along a specific axis of an object's bounding box.
Functions to calculate a bounding-box for a point surrounded by some form of radius.
Does a bounding box contain other objects?
Calculates distance between two bounding boxes.
Describes a
BoundingBox that is optionally enclosed by a larger containing BoundingBox to given padding.Calculates the extent of an object's bounding box along a specified axis.
Utility methods to create a
BoundingBox.Creates a bounding-box from one or more points.
An
AddCriteriaPair that includes marks if their bounding boxes intersect.Methods for checking intersection between a particular bounding-box and others.
Calculates the maximum coordinate of an object's bounding box along a specified axis.
Merges one or more
BoundingBox together, to create a single BoundingBox that
spans them all.Calculates the minimum coordinate of an object's bounding box along a specified axis.
Calculates the number of voxels in the bounding box of an object.
An R-Tree that contains items, each with an associated bounding-box in three dimensions.
Performs union of a bounding-box with other entities
An abstract class representing a bound with minimum and maximum values.
An outputter bound together with
OutputPattern and a generator.A bound representing physical extents, which can be resolved based on image resolution.
Attaches a replacement-strategy to a session lazily.
Abstract base class for defining bounds on rotations.
Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
Creates a randomly-generated orientation in 3D based upon Euler Angles
A bound representing unitless values, where the minimum and maximum are not affected by
resolution.
Creates a
Mask where all pixels are on within a box region.Aligns a smaller
BoundingBox to fit inside a larger BoundingBox.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.
Matches to another object, and then uses that object to bridge to another
Converts a
Stack or similar data-objects into an AWT BufferedImage.Converts a
Voxels instance into an AWT BufferedImage.Retrieves a buffer corresponding to a relative index in the z-dimension.
Creates or retrieves a byte representation of the voxels for a particular slice.
Makes a simple bytewise copy of a file, where no byte is changed.
Reuse an existing
FeatureCalculationInput, as stored in a least-recently used cache, and
without invalidating it.Creates a
FeatureCalculationCache that accepts a particular input type.Memoizes (caches) a
CheckedSupplier.Base class for functions that memoize (cache) a call to an interface.
Supplies a
LRUCache that maps a feature input-type to a corresponding to FeatureCalculationInput.An existing cache that can be used as a source for child-caches elsewhere.
A collection of existing caches that can collectively be used as sources for child-caches
elsewhere.
Derives a
FeatureInputSingleObject from a FeatureInputStack by extracting an
object mask from a specific energy channel.Derives a
FeatureInputSingleMemo from a FeatureInputPairMemo.Calculates the dilation of an
ObjectMask.Calculates a map of dilated
ObjectMasks for different iteration counts.Calculates the best-fit ellipse for an
ObjectMask using linear least squares.Calculates the best-fit
Ellipsoid for an object using linear least squares.Calculates the erosion of an
ObjectMask.Calculates a map of eroded
ObjectMasks for different iteration counts.Calculates features for objects and stores the results.
Performs calculations using child-caches instead of the main cache
Calculates a
Histogram from a specific channel in a FeatureInputStack.Calculated a histogram for a specific region on a channel, as identified by a mask in another
channel
Calculates incremental operations on
ObjectMasks and stores the results in a map.A base class for
CalculationParts that derive from an existing "delegate" calculation.Like
CalculateInputFromDelegate except assumes optional return value and no parameters.Calculates a single-input from a pair of objects.
Defines the extraction mode for the calculation.
Calculates a
FeatureInputPairObjects from a FeatureInputSingleObject and an
intersecting ObjectCollection.Calculates a threshold-level from a histogram.
Calculates a level score based on voxel intensity and a given threshold.
Base class for calculating a score based on a threshold level derived from a histogram.
Base class for
CalculateLevel implementations that operate on a list of other CalculateLevel objects.A
CalculateLevelUnary that calculates a level relative to a threshold, with an
alternative calculation method.Implementation of
CalculateLevel that calls a single delegate CalculateLevel.Calculates the number of voxels in a single object, optionally flattening in the Z-dimension.
Calculates an
ObjectMask based on a specified number of iterations.Calculates any needed orientation change.
Calculates a shell
ObjectMask by performing dilation and erosion operations.A sub-part of the calculation of a feature, that can be cached, and reused by other features.
Similar to a
CalculationPart but stores several evaluation results, differentiated by a
key.Searches a cache to reuses a
CalculationPart if it already exists.A job derived from a
Task that can be placed on different threadsLoads some images of a car.
Indicates how to arrange one or more
RGBStacks in a cell in a table.Calculates the center of gravity of a single object along a specified axis.
Maps directions to chain codes and vice versa.
A wrapper class that allows changing the output sequence for a given type.
A channel from an image.
A method of aggregating the voxels from many identically-sized
Channels into one.Base class to convert
Channels from one type to another specific type.A channel-converter that has been permanently associated with a particular object.
Converts a channel from one voxel data-type to one of multiple other types.
Converts a channel(s) at a particular timepoint into a stack(s).
Creates a
Channel corresponding to one of several data-types.Creates a
Channel with voxel-type FloatVoxelType.Creates a
Channel for a specific data-type.Creates a
Channel with voxel-type UnsignedByteVoxelType.Creates a
Channel with voxel-type UnsignedIntVoxelType.Creates a
Channel with voxel-type UnsignedShortVoxelType.Creates a
Channel to use in tests.Functional interface for creating intensity values for a given location.
Writes a single channel to a file.
Retrieves a
Channel by name from a particular time-point.A wrapper around
ChannelGetter that retrieves channels for a specific timepoint.A mapping of assigned channel-names to particular indices.
Creates a
ChannelMap for a particular OpenedImageFile.Helps retrieve channel and an associated converter and apply operation on them jointly.
Implementation of
ChannelProvider that calls two ChannelProviders that
must provide Channels of the same dimensions.Implementation of
ChannelProvider that calls three ChannelProviders that
must provide Channels of the same dimensions.Implementation of
ChannelProvider that calls a single delegate ChannelProvider.Extracts a set of
Channels from a NamedStacks, optionally resizing.Specifies a type and number of channels in a stack.
For particular child-caches, check if a
FeatureCalculationInput is available from another
LRU-cache and reuse.Like
BiConsumer but can also throw a checked exception.Like
BiFunction but can also throw a checked exception.Like
BooleanSupplier but can also throw an exception.Consumes a value and throws an exception.
Like
Function but can also thrown an exception.Like
FunctionWithInt but can also throw a checked exception.Consumes an
int and throws an exception.Like
IntFunction but can also thrown an exception.Like
Predicate but can also throw an exception.Like
Runnable but can also throw an exception.Map operations for streams that can throw checked-exceptions.
An exception that wraps another exception, but exposes itself as a
RuntimeException.Like
Supplier but can also throw an exception.Like
ToDoubleBiFunction but can also thrown an exception.Like
ToDoubleFunction but can also thrown an exception.Like
ToIntFunction but can also thrown an exception.Like a
UnaryOperator but allows an exception to be thrown.When a particular operation is unsupported in particular circumstances.
Only allows outputs, if the output-name is allowed in the
OutputterChecked.Routines for checking that particular patterns exist with bean-properties.
Strategy to determine which child-cache (among hierarchy) to employ for a particular feature
calculation.
A unique identifier for a child-cache's name commposed potentially of two elements.
Represents a 2D circle mark.
A fixture for creating circular objects and related utilities for testing purposes.
Creates object-masks that are circles in different ways
Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
Associates particular timestamp with each file, and clusters.
Uniquely identifies a cluster.
A mapping of files to membership of particular clusters.
Calculates the coefficient of
variation of all the values in the histogram.
Removes the file-name from a path, but keeps the directories and preserves the file-extension.
Writes a collection of elements as a subdirectory with each element as a single file in the
subdirectory.
Converts a RGB stack into another color space using OpenCV.
Base class for providers that draw entities (an outline or filled) on a background.
Like
ColoredBase but uses a generator to determine the colors for the objects.A collection of marks, each associated with a color.
Draws a colored representation (outline or filled) of an
MarkCollection on a backgroundDraws a colored representation (outline or filled) of a
ObjectMask on a backgroundAn
ObjectMask with an associated color.Associates a
ColorList with a ObjectCollectionDraws a colored representation (outline or filled) of an
ObjectCollection on a backgroundLike a
OverlayCollection but additionally associates a color with each overlay.Associates an RGB-color with each index.
Derives a new
ColorIndex from an existing ColorIndex applying a modulo operation
to each index call.A list of colors, each corresponding to a particular index position.
Creates a sequence of related colors.
Like
ColorScheme but employs a unary operator on a call to an existing ColorScheme.Base class for combining two masks.
Combines multiple CSV files into a single CSV file.
Several generators combined together with a common element-type.
A name which is unique when a primaryName is combined with a secondaryName
A way to combine (or not combine) objects so that they provide a feature-table.
Calculates which
VoxelDataType to use when combining two other voxel-data types, but
without losing precision.An exception thrown at run-time while processing command-line arguments.
Adds methods to
CommandLine for querying and extracting options, with and without
arguments.All command-line options used by the launcher.
A logger with additional configuration that are coupled together widely in the code.
Finds the common root directory of a set of paths.
Shared-state that exposes a common-size to all images.
A set of elements, loaded from the file-system, to be compared to another set.
Imposes an ordering on any sub-type of
Tuple3d.Imposes an ordering on any sub-type of
Tuple3i.Orders two name-values by their name (alphabetic order from standard
String.compareTo(String).Task to compare a set of annotations to a segmentation or another set of annotations.
Compares a value with a range, returning specified constants if its inside the range, below it or
above it
Like
CompareWithRange but uses features to calculate boundary valuesCompares two XML documents to see if they are equal.
A plan on which comparisons to execute for a test.
Base class for different types of projections that compare and replace each voxel.
Performs comparison of two values of type long.
Performs comparison for two values of type int.
Performs comparison of two values of type long.
Shared state for comparison operations, including grouping and statistics.
An interface for objects that can determine compatibility with a Mark.
Create a voxelwise compressed copy of any TIFF file being copied, and otherwise do a
Bytewise copy.Concatenates a list of adders.
Combines one or more
ColorProviders into a unitary ColorProvider.An
ObjectCollectionProvider that concatenates multiple ObjectCollections from a
list of providers.Combines all the channels from one or more sources (stacks, channels etc.)
Concatenates the inputs from multiple
InputManagers that all provide the same input-type.How many allocated CPUs and CPUs can be used concurrently for inference.
Monitors all submitted jobs and their current state of execution.
An instance of model that can be used concurrently for inference.
This exception indicates that an error occurred when performing inference from a model
concurrently.
Keeps concurrent copies of a model to be used by different threads.
Executes another
BinaryKernel iff a predicate is satisfied for a particular point.Singleton class for making sure Bioformats is configured configured.
Abstract base class for conic marks (e.g., ellipsoids, spheres).
Base class for conic fitters, providing common properties and methods.
Performs a binary-segmentation of the channel and converts its connected-components into objects
Converts a binary-mask into its connected components
Checks that all
Channels have the same voxel-data-type.Checks that each image has an identical set of
Channel-names, and RGB-state.Logs messages to the console, STDOUT.
A constant value that is entirely invariant to the feature-input.
A constant value for thresholding.
Always generates a constant path irrespective of the the input
Scale X and Y dimension by a constant floating-point number.
A test fixture for creating and validating feature lists with constant values.
A feature that raises a constant value to the power of another feature's result.
A path of successively-neighbored points.
The different ways of converting the voxel-data-type in a
Channel.Converts a channel by applying a converter (no histogram is involved in the conversion).
Base class for channel providers that perform conversions on a single input channel.
Creates a
ChannelConverter for converting a channel to a particular type.Creates a
ChannelConverterAttached<Histogram, T> for converting a channel to a particular
type, making use of a Histogram.A converted-input, together with any logged messages associated with it.
Converts an
ImagePlus into a channel or voxels.Convert from the OpenCV
Mat to a Stack.Converts a feature from physical volume units to voxel units.
Converts each input-image to an output format, optionally changing the bit depth.
Converts
NamedChannelsInput to a variety of others to match a delegate task.An input object that converts
NamedChannelsInput to StackSequenceInput.Manager that converts (one channel)
NamedChannelsInput to StackSequenceInput.Converts a RGB image to the HSV color
space.
Converts a RGB image to the Lab color
space.
Converts a subset of raw voxel bytes in a buffer to a possibly a buffer with different data-type.
Creates a
ConvertTo to match the desired voxel-type.Converts a channel or voxels into a
ImagePlus.Converts other voxel data-structures (as used by Anchor) to an ImageJ
ImageProcessor.Converts common image data-structures used by Anchor to the
Mat class used by OpenCV.Converts a feature value representing area in pixel units to physical area units in an isometric
XY plane.
Converts a distance feature to physical units along a specified direction.
Converts a feature value representing volume in voxel units to physical volume units.
Converts a
ImageProcessor to a voxel-buffer of particular data-type.Converts a feature value from one unit type to another.
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
Calculates a 3D convex hull from a binary mask.
Base class for convex hull implementations.
Utility methods for calculating convex hulls on 2D points.
Context parameters when copying many files from a source directory to a destination directory.
Copies the bytes from a
IFormatReader to a list of channels, converting if necessary.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. bytewise or activating compression etc.).
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.Stores costs between all possible pairings between elements from two lists.
TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
The sum of the results from a particular feature.
Counts the number of items in a histogram (posssibly in relation to a threshold: above, below
etc.)
A projectable buffer that also keeps track of the number of voxels in it.
Counts the number of voxels in an object that have a specific intensity value in a channel.
A simple counter that increments.
Counts the number of intersecting voxels where bytes are encoded as region memberships.
Base class for kernels that return a count (positive integer) for every voxel.
For every voxel on the outline, count all neighbors that are adjacent.
The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an
ObjectMask.Like
IterateVoxelsBoundingBox but counts voxels matching a predicate rather than
iterating.Like
CountVoxelsIntersectingBounded but specifically counts areas of intersection between
two ObjectMasks.A generic exception that be thrown when the creation of a new object fails.
Creates a mark by fitting it to a set of points extracted from other marks.
When creating a model to be used for inference fails.
Creates a model to use in the pool.
Creates a new channel with all values initialized to a constant (by default zero)
Creates a new empty collection of marks
Converts a
BufferedImage from the AWT library to a Stack.Compares two CSV files to determine if they are identical or not.
A generator that writes the contents of a CSV file to the file-system.
Reads a CSV File from the file-system.
Reads a CSV file line-by-line.
When an error occurs reading a CSV file.
Writes a CSV file to the file-system.
This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the
threshold into the bin just below the threshold value
The bounding box is filled apart from cuboids cut out of the corners
Creates one or more objects that are otherwise rectangles with on values, but with corner
voxels as off.
Wrapper around OpenCV's findContours
function.
Provides for initialization of the JavaCPP bridge to OpenCV.
The maximum-intensity allowed by the data-type of the stack.
How to style a date in a file-name.
Executes different processors depending on whether we are in debug mode or not.
An alternative mode of option where behaviours change.
Extracts text from a RGB image by using the EAST deep neural network model and the ONNX
Runtime.
Decodes inference output into segmented-objects.
Decodes a labelled raster into derived objects or object-like elements.
Creates an element from the scaled-object and its index.
Decodes the inference output from a Mask-RCNN implementation.
Ensures each object in a collection is a connected-component, decomposing it if necessary into
multiple objects.
A default set of
ReadOptions without special behavior.The default strategy for finding children by always directly taking (or creating a child-cache)
as necessary.
Indicates a default bean-instance is available.
A bean where the definitions of many different
NamedBeans can be specified.Specifies a list of features directly without assigning any custom-naming.
Indicates that an object can add one or more items to a
Define.Base class for
AnchorBeans that can add items to a Define.Like
DefineAdderBean but adds a prefix to the name of beans when adding.Called when a bean fails to be added to a
Define.Specifies features via a list of names and associated with features.
Creates a new
Define.Applies a
Define on inputs and outputs produced entities (images, histograms, objects
etc.).Functional interface for processing an
ImageInitialization.Like a
Define but outputs also an energy-stack.Functional interface for processing with an energy stack.
Specifies a single feature directly without assigning any custom-naming.
A base class for features that operate on a derived object mask and calculate a feature on it.
Embeds each feature in a
FeatureDeriveFromPair feature (first, second or
merge) and prepends with a string.Derive an
ObjectMask by incrementally adding points.Derives a path from an existing path.
When an error occurs deriving a path from another path.
Generates report of the execution-times of different operations.
Builds string-descriptions of a
NeighborGraph.Labels images based on whether their descriptive name contains a specific string.
When a deserialization operation fails.
Creates an object from a serialized representation on the file-system.
Selects a destination-channel for the byte-copier, given an index
Derives various types of outputs (images, histograms etc.) from
MultiInputs.Collection of parameters represented by key-value pairs.
Base class for beans that require initialization with
DictionaryInitialization.Checks if a value in a
Dictionary is equal to an expected value.Deserializes a
Dictionary from a file-system representation as a Java properties file.A generator that writes the contents of a
Dictionary to the file-system as XML.Initialization parameters that provide a named-mapping to
Dictionarys.Base class for beans that implement
Provider to provide a Dictionary.References a particular
Dictionary in shared-object-space.Similar to
Difference but calculates the width as the standard-deviation of the histogramPerforms a dilation morphological operation on
BinaryVoxels.Dilates each object in the collection, growing bounding-boxes as necessary in relevant
dimensions.
Additional parameters for influencing a morphologicla dilation opperation.
Morphological dilation with a 3x3 or 3x3x3 kernel size.
The size of an image (in voxels), together with the image resolution.
Utility class for checking and ensuring consistency of dimensions across channels and masks.
Infers
Dimensions for a particular image-file.Base class for beans that implement
Provider to provide Dimensions.A vector indicating a direction in space.
A bean that creates a
DirectionVector.Options that influence how an output directory is created.
Creates necessary directories on a file-system to make a path valid.
Lists all directories to a certain depth
Reuses the directories between a path and its root to form the output - and also the filename.
A directory into which files can be written, and a prefix for the name of each written file.
Calculates features values for all objects, and discards any object less than
quantile - (minRatio * stdDev)Stack that contains 1 or 3 channels so that we and display it as either grayscale or as an RGB
unsigned 8-bit image, respectively.
Writes a display-stack to the filesystem.
A
BeforeCondition that checks if two ObjectMasks are within a specified maximum
distance.Implementation of
UnitValueDistance that specifies a value in physical units, as
described by particular recognized strings.Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
Like
DistanceTransform3D but applies the distance transform separately for each object in
a collection.Implementation of
UnitValueDistance that specifies a value in voxels, ignoring any
physical image resolution.A feature that divides the results of multiple features sequentially.
A feature that divides the result of another feature by a constant value.
Creates a line of text that span a certain width with a repeated character, optionally containing
a label.
Like
BiPredicate but operates on doubles.A bean defining a list of
Doubles.Creates a
DoubleList from a XML element.A bean defining a set of
Doubles.Creates a
DoubleSet from a XML element.Utilities for arithmetic operations involving type
double.Outlines or completely fills in each
ObjectMask with a color.Similar to
DrawObjectsGenerator, but with the background stack cropped to focus only on
the region containing objects.Draws a lines between successive points on the convex-hull of an object.
Draws a representation of an
ObjectMask on a RGBStack.Creates images of object(s) drawn on a background only in a local region around their bounding
box.
Generates stacks of RGB images using a
DrawObject to draw objects on a background.Draws an ovleray onto a
RGBStackAllows for comparison of objects that exist on different test loaders
Factory for creating
DualComparer instances to compare directories.Two mark-collections, one considered accepted and the other rejected.
An annotation that consists of two sets of marks, accepted and rejected.
Deletes
DualMarksAnnotations from the file-system.Writes
DualMarksAnnotations to the file-system.A
Predicate<Path for both a file and a directory.Stores two versions of the same object, representing two different scales.
Creates a duplicate of the input channel.
A provider that creates a duplicate of a given
Mask.Duplicates (deep copy) an object-collection.
Selects features and objects directly from the input list, treating each object independently.
Evaluates items immediately via the
StoreSupplier as soon as they are added.Applies an edge detection filter to each slice of a
Channel independently using ImageJ's
FIND_EDGES filter.An eigenvalue and its corresponding eigenvector.
Outputs an element to the file-system.
Creates or gets a element to output files together with a
ElementWriter.Writes an element (with or without an index) to the file system.
Creates or gets a element-writer to output files.
Represents a 2D ellipse mark.
Extracts forms for 'standard form' representation of an ellipse from the coefficients for a 2nd
order polynomial describing the ellipse.
Represents a 3D ellipsoid mark with multiple sub-regions.
Base class for features that calculate properties of an
Ellipsoid fitted to an object.Factory for creating
Ellipsoid objects using least-squares fitting.Helper class for fitting ellipsoids to point data.
Calculates the ellipsoidicity of an object by fitting an
Ellipsoid to it.Utility class for operations related to Ellipsoid marks.
Calculates the ellipticity of an
ObjectMask (on the center of gravity slice if it's a
z-stack).Creates an empty object-collection.
Specifies a constant if a histogram is empty, otherwise delegates to another {#link
org.anchoranalysis.image.bean.threshold.CalculateLevel}
A wrapper around
UnsignedIntBuffer that provides methods for encoding and decoding
watershed-related information.An interface for encoding a 3D direction into an integer representation.
Represents voxels encoded with watershed-related information.
A collection of memoized marks on which energies can be derived.
Represents a pair of
Marks with their associated total energy.Saves and manages the total energy for all items in a collection.
Stores and manages individual energy values for a collection of marks.
Stores and manages pairwise energy interactions between marks.
The energy for a feature-list as factorized into different cliques.
An abstract class for creating
EnergyScheme instances.Creates an
EnergyScheme by combining individual elements and their interactions.A set of
EnergySchemes, each associated with a unique name.Combines an
EnergyScheme with SharedFeatures for energy calculations.A
EnergyStackWithoutParameters with associated parameters in a Dictionary.A fixture for creating
EnergyStack objects for testing purposes.A stack of channels used as context to calculate features (or calculating energy more
broadly).
Writes an energy-stack to the file-system.
Represents the total energy of a system, which can be modified and queried.
Returns true if two values are equal, and false otherwise.
A relation
double1 == double2.Performs an erosion morphological operation on
BinaryVoxels.Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
A feature that erodes an object mask and then calculates another feature on the eroded object.
Erosion with a 3x3 or 3x3x3 kernel size.
An abstract class representing a node in an error tree structure.
An exception that adds a string to the current error node.
A singleton implementation of ErrorNode that does nothing with errors.
Reports errors as they occur.
Utility base class for common error-reporting formatting.
An error-reporter that replaces particular errors/exceptions with user-friendly messages.
Records errors, by writing them into a logger.
Logs error messages into a
String via StringBuilder.Excludes all inputs whose identifiers match a regular expression.
Executes a task on a single-input outputting into a specific directory.
Arguments that can further specify an experiment's execution (in its entirety) in addition
to its bean specification.
Records the execution-time of particular operations.
Creates an instance of
ExecutionTimeRecorder depending in what outputs are enabled.An implementation of
ExecutionTimeRecorder that is a simple placeholder that does
nothing.A base class for a type of task that produces some kind of result of interest.
An exception that occurs when an experiment is executed.
Runs a particular experiment after identifying necessary paths and input files.
Creates an
ExperimentExecutor.SelectParam<Path> factory for experiments.Objects to give the user feedback about different aspects of the experiment.
A method to produce an identifier for an experiment.
Automatically populates a experiment-name and version number
Defines constants for name and version of an experiment
Launches an experiment by calling the application 'anchor' via the shell.
Calculates features and exports them as a CSV file.
Visual style for how features are exported.
Exports a histogram of voxel intensities as a CSV file for each channel of an image.
An interface for exporting shared objects to a target container.
Creates a 3D version of an object by replicating each input-object across the z-dimension to meet
(3D) dimensions.
Extends an object (2D/3D) as much as it can within the z-slices of a containing object
Utility class for adding file extensions to filenames.
Remembers each unique extension, and associated count
Extracting a file-extension from a path according to rules.
Width/height/depth of energy-stack in pixels depending on axis.
The sizes: width, height, depth etc. of an entity in 2 or 3 dimensions.
Checks if the
Extents of two BoundingBoxes are identical.A particular
Extent to be arranged, with calculated aspect-ratio, and its unique index
position.Finds the exterior outer contour for a
Mask that forms its outline.An iterable-generator that outputs the portion of a stack corresponding to a bounding-box
Extracts the slice at the center (rounding down) of the range of z-stacks.
Extracts one type of parameter from another, if possible.
Exposes a
NamedProviderStore<TimeSeries> as a NamedProviderStore<Stack> by
extracting a frame from each series.Extracts the identifier from an
InputFromManager to summarize further.Extracts the identifier and path from an
InputFromManager to summarize further.Extracts a
Point3i representing the mid-point of an ObjectWithProperties.Extracts a
Path from an input to summarize further.Extracts a range of elements from a
Path.Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.
Extracts slices from
sliceStart (inclusive) to sliceEnd (inclusive).Extracts three channels to make an RGB image.
Writes text to a file, but only if
FailureOnlyMessageLogger.close(boolean, boolean) is called with successful==true.Base class for a measurement that calculates a result (double) given input parameters.
An abstract base class for features that operate on
FeatureInputAllMemo.A base class for a
Feature that is a binary-function of the results from two other
features.A context in which to calculate features while caching certain duplicated internal calculations
among the features.
The context in which features are calculated, so as to be later exported as a CSV.
When the calculation of a feature cannot complete successfully.
Gives a
FeatureInput the necessary context for feature-calculation, including associating
it with a cache.Calculates
FeatureCalculationInput when passed a particular Feature and
corresponding FeatureCalculationInput.Adds a cache to a
FeatureCalculatorSingle or FeatureCalculatorMulti.Calculates feature or feature values.
Like a
FeatureCalculator but is permanently associated with one or more Features.A
FeatureCalculatorMulti but changes the input before calculation.Utility class for extracting an
EnergyStack from a StackProvider.Like a
FeatureCalculator but is permanently associated with a single Feature.A
FeatureCalculatorSingle but changes the input before calculation.Exposes a
FeatureCalculatorMulti as a FeatureCalculatorSingle.An abstract base class for features that convert units between physical and voxel space.
Assigns an objects from one set of objects to another based upon a cost (degree of overlap).
Needed non-result information to output a feature-values CSV file.
Like a
FeatureCSVMetadata but additionally associates an output-name.Writes the results of feature-calculations as a CSV file.
To facilitate creation of a
FeatureCSVWriter from corresponding FeatureCSVMetadata.Base class for evaluating
FeaturePairObjects in terms of another feature that operates on
elements (first, second, merged etc.).A base class for features that only require an input that extends from
FeatureInputEnergyA feature that uses a channel from the energy-stack as identified by an index.
Defines a feature and provides a means to calculate inputs for it, a session.
Shared-state for an
ExportFeatures task.Context for exporting features, containing configuration and output settings.
A base class for a
Feature that is a function of the results from a list of other
features.Base class for features that broadly accept any type of feature-input.
A base class for features that accept a histogram as input.
Base class for
FeatureHistogram implementations that calculate a statistic from the
Histogram.A base class for a feature that accepts a
FeatureInputImageMetadata as input.Parameters used to initialize a
Feature before any calculation occurs.A single input used for feature-calculation to produce a result.
Feature input that contains a list of memoized energy calculations for all marks.
A
FeatureInputWithResolution that has an optional associated Dictionary.A
FeatureInput that exposes the Dimensions of an image or scene.A
FeatureInputDimensions that has an optional EnergyStack associated with it.A feature input that contains a histogram and optional resolution information.
A
FeatureInput that provides ImageMetadata.A feature input that wraps a
Mark along with optional dimensions and dictionary.Feature input that contains a collection of marks and optional dimensions.
A
FeatureInput with no associated parameterization.A feature input representing a collection of objects, optionally associated with an energy stack.
A fixture for creating FeatureInputPairObjects with circular object masks.
Feature input that contains a pair of memoized voxelized marks and an energy stack.
A pair of objects (first and second) and optionally a merged version of both.
A
FeatureInput with the stored results from a prior feature-calculation.Feature input that contains a single memoized voxelized mark and an optional energy stack.
An input representing a single object-mask (with maybe an energy-stack associated).
A feature input that represents an energy stack.
Performs checks and aggregations on feature-input types are compatible with others
A
FeatureInput that exposes the Resolution of an image or scene.An abstract base class for features that calculate values based on intersecting objects.
A feature that calculates a value based on intersecting objects, considering each intersecting
object individually.
An abstract feature that calculates a value based on intersecting objects, considering each
intersecting object individually and applying a threshold.
A list of features with the same input-type.
Defines a list of features and provides a means to calculate inputs for it, a session.
Factory for creating
FeatureList in different ways.Provides a list of
Features with identical input-type.Calculates features on each part of a pair (first, second, merged etc.) and then reduces the
calculation to a single number.
A list of
Strings representing feature names.A map of feature-names (strings) to indexes (int).
A base class for a feature that accepts a
ObjectCollection as input.Information needed for the outputting differnt types of feature-table CSV files.
The customizable output names used by
LabelledResultsCollector, which all follow a
pattern based on a prefix.An abstract base class for features that operate on pairs of memoized objects.
An abstract base class for features that operate on pairs of objects.
Provides a single
Feature.Defines a single
Feature to provide via a bean property.Provides an existing
Feature identified by its name and optionally a feature-list in
which is resides.Beans-related to
Features, and which require initialization with FeatureRelatedInitialization.Parameters for initializing a
FeatureRelatedBean.Features that process
ResultsVectorList.A collection of results from feature calculation, and associated thumbnails.
Base class for an instance of
FeatureResults that calculating a statistic across all
results in the ResultsVectorList for a particular feature-value.Supplies the result of a feature calculation.
A single-point in the code for creating feature-sessions (a factory).
A fixture for creating feature lists and feature list providers from XML files.
An abstract base class for features that operate on a single memoized object.
An abstract base class for features that operate on a single object.
Calculates object-masks from entities in shared, using the feature-input only for an
energy-stack.
Extracts features from some kind of inputs to produce one or more rows in a feature-table.
An abstract base class for features that operate on image stacks.
Resolves and calculates a feature by a symbol.
A feature-calculator with additional functions for encoding the output in a tabular format with
column names.
Base class for a
Generator that outputs a feature-table in CSV format.Creates a
FeatureTableCSVGenerator.Utility class for testing feature calculations in a controlled environment.
Utility class for testing features with both positive and negative cases.
A feature that contains another feature as a bean-parameter.
A
FeatureUnary that accepts any FeatureInput irrespective of type.Utilities to access a
Field of an AnchorBean.A file-format that is read or written to the filesystem.
Creates a
FileFormat from a string.An input pertaining to a single file on the file-system.
A map that associates file identifiers with labels, typically loaded from a CSV file.
Associates a name (a compact unique identifier) with a file.
Provides useful additional objects when assigning a name to a file.
Base class for methods that derive the name independently for each file.
A file-name with the base (without extension) split from the extension.
Base class for beans that require initialization with
FilePathInitialization.Initialization parameters for a named-set of file-paths.
Matches file-paths against some kind of pattern.
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.
Calls an existing
FilePathProvider indirectly to provide an identical result.Conversion to Unix-style separators.
Tracks the range of file-size.
Base class for providing a list of
Files.When an error occurs providing a set of files.
Like
FilesProvider but employs a unary operator on a call to an existing FilesProvider.Base class for implementations of
FilesProvider which do have an associated
directory.A
FilesProviderWithDirectory where the directory is optionally specified as a string
constantLike
FilesProviderWithDirectory but employs a unary operator on a call to an existing
FilesProviderWithDirectory.Base class for implementations of
FilesProvider which do not have an associated
directory.An input pertaining to a single file on the file-system - and a directory in which it resides.
Montages
Extents together to completely fill the available space, while preserving aspect
ratio.Draws a filled-in shape for each object.
Fills holes in a mask, with options to skip holes touching the border or exceeding a maximum
volume.
Fills holes in an object.
Filters an
ObjectCollection using the specified ObjectFilter.Applies an object-filter to the results of an upstream segmentation.
Filters an
ObjectCollection by grouping objects and then applying a filter to each group.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.
Helper class for applying filters to
Channels and BinaryVoxels using ImageJ
operations.Filters a list of inputs when in debug-mode
Rejects files that fail to match a particular regular-expression
Finds a common voxel-data type to represent two types.
Finds contour voxels, the pixels forming a continuous path along the boundary of the object or
mask.
When an error occurs finding files.
Evaluates a feature on the first object in a pair of objects.
Fits a box around the on voxels.
Scales the size of images to match the target image, preserving aspect-ratio.
A
MarkCollectionProvider that fits points from objects to create marks.Represents the result of fitting an ellipsoid to a set of points.
Scales an image to approximately similar in size to a
SizeXY.Performs a flattening (maximum intensity projection in each channel) of the output of another
writer
Combines all series and frames returned by a reader by converting them into multiple channels in
the same image.
Like a
StackGenerator but first applies a maximum-intensity-projection.Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity
projection).
Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity
projection).
Convert to a float buffer, given an unsigned-byte source buffer.
Convert to a float buffer, given an unsigned-int source buffer.
Utilities for arithmetic operations involving type
float.A 32-bit voxel data-type representing floating-point numbers, as per the Java primitive
float type.
Creates an object for each separate intensity-value (beginning at
startingColor) by
flood-filling.Forces the bits per pixel to be a specific-value, irrespective of what bioformats infers.
Forces the number of channels to be a specific-value, irrespective of what bioformats
infers.
Forces the number of frames to be a specific-value, irrespective of what bioformats
infers.
Treats a time-series as if it was a z-stack
File extensions for various formats.
Dimensions-calculation for one specific axis only.
A positive-result when an object is found at a particular location.
Helper methods to test a
RasterWriter on stacks with between 1 and 4 channels.Counts the frequency of certain strings, and describes the contents in human language.
Converts certain exceptions that occur from XML-Parsing into a friendly form to display to the
user.
Provides files associated with annotations.
Implementation of
SliceBufferIndex with voxels of type unsigned byte.Creates image-dimensions by referencing them from a
ChannelProvider.Creates a mask from an existing channel, reusing the channel's buffer and considering all 0
values as off, and 255 values as on.
Base-class for
MaskProviders that accept a Channel as input.Derives the grouping-key via a call to
DerivePath.The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create
an output prefix.
Extracts a key-value from a
Dictionary as a double.An abstract base class for features that require a
Dictionary for initialization.An abstract base class for creating a channel from specified dimensions.
Base class for
MaskProviders that create a mask based on given dimensions.Base class for features that are calculated from
Dimensions.Extracts a path from a
FilesProvider.Implementation of
SliceBufferIndex with voxels of type float.Each input-file describes a histogram that produces one row of features.
Calculates features from a single image.
Calculates features from the metadata from single image.
Finds the input-stack using a conventional name of
input_image - and extracts the first
channelFinds the input-stack using a conventional name of
input_imageImplementation of
SliceBufferIndex with voxels of type unsigned int.Specifies a list of colors by a list.
Creates object-masks from a
MarkCollection where (a particular region of) each mark
creates an object.Converts a binary-mask to an object-collection (containing a single object)
A base class for a
ChannelProvider which also uses a binary-mask, but which doesn't use
any other ChannelProvider as an input.Creates a
Mask from a collection of object-masks.Implementation of
SliceBufferIndex with voxels of type unsigned short.A single color repeated to meet the size.
Creates a
MarkCollection from a single mark provided by a SingleMarkProvider.Extracts a channel from a provider of a stack.
Creates a
Mask from a specific channel in a stack.Uses a
StackReader to read the image-metadata.Selects a subset of channels from a set of stacks.
Adds a list of Named-Items define in a XML file in the current directory.
Utilities for repeating operations a certain number of times.
Utility functions for manipulating or creating
List in a functional way.Like
FunctionalList but executes any operations in parallel where possible.Like
Function but also accepts an int parameter.Applies a 2D Gaussian blur filter to each slice of a
Channel independently.Calculates a score between 0 and 1 based on the Cumulative Distribution Function (CDF) of a
Gaussian distribution.
Generates colors to match the size of an object-collection.
Objects that must implement well-defined
equals() and hashCode() methods and also
generate a name uniquely identifying the class and all parameterization.A class that writes a particular type of object(s) to the filesystem.
Exposes a
Generator<T> as if it was an Generator<S>.Settings and methods for writing to the filesystem from a generator.
When a get operation fails for a particular key.
Defines global identifiers for different regions of a mark.
Extracts a glob from a string describing it, and a direcory which gives it context.
A string describing a glob, associated with a directory onto which it will be applied.
Base class to calculate the gradient of the voxels in a
Channel.Like
GradientBase but allows an arbitrary constant to be added to voxels storing the
gradient.Extracts the gradient in the direction of a particular axis (identified by an index)
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
Calculates a
Channel's gradient along the x and y axes.A logger for graph operations, using a
DescribeGraph to generate descriptions.A graph, either directed or undirected, where edges contain no payload.
A graph, either directed or undirected, with edges containing a payload of type
E.Performs 2D grayscale reconstruction using ImageJ's implementation.
Abstract base class for performing grayscale reconstruction by erosion.
Implements grayscale reconstruction using Robinson's algorithm.
Only accepts an object if it has greater (or EQUAL) intersection with
objectsGreater than
objectsLesserReturns true iff
valueFirst is greater than valueSecond.A relation
double1 > double2.Returns true iff
valueFirst is greater than or equal to valueSecond.A relation
double1 >= double2.Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the
threshold
A set of
AnnotationLabels partitioned into their unique groups.Stores feature-calculation results, indexing by their group.
Commonality between shared state for grouped export tasks.
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
Determines how partition inputs into groups.
An
InputManagerWithStackReader that can unify separate images in separate files to form a
single Stack.Indicates that a set of definitions of classes can be collectively grouped using this class.
Adds items to aggregate structures identified uniquely by a name, and allows these items to be
later outputted.
Grow the bounding-box to fill
larger as much as possible.Guesses dimensions from an input-image if it exists.
Methods for extracting a user-friendly error description.
A simple scheme for counting the touching voxels.
A generator that writes a
ObjectCollection to a HDF5 file.Paths to identify objects in the HDF5 for object-masks.
Populates
ImageMetadata from the header of an image-file.A dummy task that simply writes a message to all log files, specifically: 1. log file for
experiment 2. log file for each input-object
Configuration for help messages in the launcher.
A histogram of integer values.
Consumes a bin and corresponding count.
Writes a histogram to a CSV file.
Reads a CSV file from the file-system that describes a histogram of voxel values.
Creates a
Histogram to describe the intensity values of voxels in aggregate.A fixture for creating predefined histograms for testing purposes.
Create a
Histogram of the voxel intensity values in an image, pertaining to a region
defined by a ObjectMask or a Mask.Implementation of
HistogramProvider that calls a single delegate HistogramProvider.Further statistics that can be derived from a histogram in addition to those existing as direct
methods of
Histogram.Utility class for thresholding histograms.
Creates the entire HOG descriptor for an image.
One part of a Histogram
of Oriented Gradients descriptor, as applied to an image stack.
Parameters for calculating a HOG Descriptor covering window-size, block-size etc.
Creates a
FeatureCalculationCache which caches the results of calls to features, even if
the same feature appears multiple times, directly or indirectly.Creates a sequence of colors by varying the hue-component in a HSB color
model.
An implementation of the Hungarian algorithm for solving the assignment problem.
Gets a unique identifier for a particular element at a particular iteration point.
Builds an identifier (a filename without extension) for a saved-raster corresponding to certain
properties.
Identify an element uniquely only by its iteration timepoint.
Assigns a unique id number to each object.
Returns the same
Path as the argument passed in.A voxel score that can optionally normalize and adjust the intensity values.
A voxel score that imposes a value relation to a histogram.
The result of featureCondition is compared to a threshold, and then either the underlying feature
is calculated (positive case), or featureElse is (negative case)
Calculates a value if a condition lies within a certain range, otherwise returns constants
Branches to two different
DrawObject depending on a predicate.Interface for the condition that is tested, to determine which
DrawObject to use.Calculates a level from the first delegate and if greater than a threshold, recalculates from a
second delegate.
When a
IndexRangeNegative is passed as an argument, an InputGrouper is
constructed that extracts elements from a Path.Outputs the logical operation
iff first==HIGH and second==LOW then LOW voxelwise on both
masks, modifying {mask} with the result.Multiplexes between two
PathPrefixers depending on whether an incrementing number
sequence was output was requested.The current
mask is returned if a condition on key-values is satisfied otherwise
maskElse is returned.Calculates a level from the first delegate and if less than a threshold, recalculates from a
second delegate.
The current
mask is returned if it's non-empty (at least one on voxel) otherwise
maskElse is returned.The current
mask is returned if the mask (treated as an object) passed an object-filter,
otherwise maskElse is returned.Clamps a feature value if it lies outside a specified range.
Multiplexes between two object-collection-providers depending on whether a parameter value equals
a particular string
Provides a channel based on a condition from a dictionary.
Base class which multiplexes between the current mask and an alternative depending if a condition
is met.
Multiplexes between two namers depending on if the relative-to-directory option is
selected.
The current
mask is a particular stack exists (at least one on voxel) otherwise
maskElse is returned.Creates a new channel which is a merged version of two input channels according to rules.
All outputs are allowed unless the name's first character is an underscore.
Like
IgnoreUnderscorePrefix for all first and level-outputs unless a particular outputs
are explicitly specified.Assigns a label to each image and copies into subdirectories for each label, and creates a
labelling CSV.
A bean that must be initialized with
ImageInitialization before usage.Base class for a method comparing two image files.
Counts images on aggregate, some with associated annotations, others without.
Allows operations to be applied to several
ImageCounters collectively.Like
ImageCounter but also exports statistics.Labels images based on a CSV file containing image identifiers and corresponding labels.
Initialization data for an image CSV labeller.
Timestamps and other metadata associated with an image file-path, but not with the file's
contents.
How values are encoded into an image-file.
A type of image format that are read/written to the filesystem, together with the extensions it
may use.
How to shape the image (across various dimensions) after the copying
Attributes describing the situation in which inference on images is occurring.
A model used for inference that accepts an image as an input.
The state used to initialize a
ImageBean.Creates instances of
ImageInitialization based upon an InputOutputContext.When an error occurs reading or writing an image to/from the file-system.
Resizes with linear
interpolation as implemented in ImageJ.
When conversion to ImageJ data/type is not possible, or an error occurs during conversion.
Base class for writing a raster using ImageJ.
A single label that is associated with an image.
Reads an
ImageLabelAnnotation from the file-system.Writes an
ImageLabelAnnotation to the file-system.Associates a label with an image.
Maps one set of labels to another
Assigns a single label per image, as a whole.
Information about an image, but not about the intensity or content of image voxels.
An input that provides a
ImageMetadata but only lazily when first called.Reads an
ImageMetadata from the file-system.The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of
points.
A base class for features that are calculated using image-moments.
Metadata to describe a pyramid-representation of
images, if at least one exists in a file.
Summarizes the size of images.
Reads the size of each image initially, before normal (parallel) task execution.
A suggestion on a size for an image.
Creates a
ImageSizeSuggestion.This combines
ImageFileAttributes plus a timestamp for image-acqusition.Derives
ImageTimestampsAttributes from a file, additionally checking for EXIF metadata.Resizes with an interpolator that uses Lanczos resampling as implemented in
Imglib2.
Resizes with an interpolator that uses linear interpolation as implemented
in Imglib2.
Imposes minima in seed locations on the input-channel before performing the segmentation
Adds an explicit
Resolution to an image after it has been read.Defines an
AnchorBean in a separate file on the file-system.Like
ListBeanFactory but also includes elements in other lists defined in the
include tag. as elements.Exception thrown when there's a failure in including marks during the add criteria process.
When an image has incompatible image-size with expectations.
When an unexpected
VoxelDataType is encountered.An
AfterCondition that checks if merging two ObjectMasks increases a specific
feature value.Outputs an incrementing number for each output that occurs.
Converts each channel independently and creates a single-channeled stack from the conversion.
Holds a single-index which is hashable and comparable.
An
Indexable object that contains MarksWithEnergyBreakdown.An output-name with an index somehow appended or prepended in a particular style.
An index structure that organizes voxel partitions by channel.
An index structure that organizes voxel partitions by region and slice.
A particular
Channel to be read from a file, identified by its position (index) in the
file.A range of discrete integers with a minimum and a maximum.
Specifying a sub-range of indices, tolerating also negative indices.
Creates
IndexRangeNegative.A range of discrete integers, where one can always find the succeeding or preceding index.
A model used for inference.
Tries to construct the
ImageMetadata from EXIF and other metadata, if available, or
otherwise falls back to another reader.A bean that must be initialized with some parameters before being used.
Context for creating initialization-parameters.
A factory for creating FeatureInitialization objects.
Factory for creating
ImageInitialization instances.Assigns a parameter to a bean, if the bean accepts it.
Combines
ImageInitialization with an EnergyStack.An exception that occurs when initializing something, and it doesn't succeed
Arguments that can further specify an experiment's input in addition to its bean
specification.
Input for executing a task, associated with shared-state and other parameters.
Additional parameters that offer context for many beans that provide input-functions.
SelectParam<Path> factory for inputs.One particular input for processing.
A base class for
InputFromManager-implementing classes that delegate to another.Derives a grouping key from an input.
Base class for describing the inputs.
Parameters passed to an
InputManager to generate input-objects.Base class for an
InputManager that delegates to another InputManager with the
same input-type.Extends an
InputManager to add a StackReader bean property.A context for performing input generally and outputting to a particular output-directory.
A fixture for creating
InputOutputContext instances for testing purposes.This exists as an implementation of
InputOutputContext that exposes a StatefulMessageLogger.Caches a
InputOutputContext for each subdirectory as they are created.An experiment that uses both an
InputManager to specify inputs and a OutputManager to specify outputting.When an error occurs reading an input.
All inputs for an experiment, together with any parent directory which is specified as a parent
for these inputs.
A list of base (parent) classes for input-types that a task expects.
Generates an out string where $digit$ is replaced with the #digit group from a regex
Base class for testing implementations of
SegmentStackIntoObjectsPooled.Exception thrown when there are not enough points to perform a fitting operation.
Like
IntPredicate but accepts two arguments.A bean defining a list of
Integers.Creates a
IntegerList from a XML element.A bean defining a set of
Integers.Creates a
IntegerSet from a XML element.Outputs a file-name involving an integer suffix of length
numberDigits with leading
zeros.Calculates a statistic from the intensity values covered by a single object-mask in a channel.
The intensity of a particular channel of the stack, by default the mean-intensity.
Base class for features that calculate intensity gradients from multiple channels.
Only keep objects where at least one voxel (on a particular channel) has intensity greater or
equal to a threshold.
Utility class for calculating mean intensity of objects in a channel.
Calculates the maximum mean intensity across all slices of an object in a channel.
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
Constructs a shell around an object-mask using a standard dilation and erosion process.
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including
the original object-mask) and measures the mean intensity of this shell
Calculate various moment-related statistics about the intensity of each channel of an image.
Implementation of
StackDisplayer that converts to unsigned-8bit by taking the upper and
lower quantiles of the intensity range.Converts a
Channel to UnsignedByteBuffer by scaling against the maximum
intensity value that appears in it.Defines a particular type of interpolation method that can be used for resizing images.
A fixture for generating collections of intersecting and non-intersecting circular objects.
A data-structure to efficiently determine which object-masks intersect in a collection.
An
ObjectMatcher that matches objects based on their intersection with a provided set of
objects.Finds the intersection of two objects and calculates a feature on it
Calculates the intersection-over-union
score for a pair of bounding-boxes.
Keeps objects which intersects with ANY ONE of a collection of other objects.
Returns only the objects that intersect with at least one object in the container
An R-Tree that contains items, each with an associated one-dimensional interval.
Represents a function that accepts an int-valued argument and produces a float-valued result.
An exception thrown if an invalid path is inputted as an argument.
Inverts the intensity values of a
Channel by subtracting each voxel from the maximum
value for the channel's data type.Switches on voxels to off and vice-versa.
Invert the
ScaleFactor calculated by the scaleCalculator delegate.Performs a segmentation and inverts and on and off bytes
Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
Routines to iterate a
Kernel over some or all of the voxels in a BinaryVoxels.Utilities for iterating over all voxels in one or more
Voxels.Utilities for iterating over the subset of image voxels within a bounding-box.
Like
IterateVoxelsAll but specifically for equal-to operations on Voxels of type
UnsignedByteBuffer.Like
IterateVoxelsBoundingBox but specifically for processing areas of intersection
between BoundedVoxels of type UnsignedByteBuffer.Utilities for iterating over the subset of voxels corresponding to an on state in a
Mask.Utilities for iterating over the neighboring voxels to a given point.
Utilities for iterating over the subset of voxels corresponding to an on state in an
ObjectMask.Utilities for iterating over the subset of voxels corresponding to an on state in an
optional
ObjectMask.Utilities for iterating over remaining voxels in one or more
VoxelBuffers.A description of the job's name and associated number.
An exception that occurs when a job is executed.
Base class for a method to apply a task on inputs.
Logs events when jobs start and stop, with or without errors.
Monitor execution-state of a job, and how long it is taking/took to execute.
Generates an outstring of the form
The headers found in a JPEG file.
A small matrix that is convolved with or otherwise combined across each voxel in an image.
Parameters used for applying a
Kernel to a BinaryVoxels.A mutable context around determining whether a particular point should be on or off
with a
BinaryKernel.Calculates the kurtosis of all the values in
the histogram.
Headers in a CSV file for the non-results (i.e. labels) part of a feature-row
Generates a list of header-names for columns unrelated to features (identifiers and groups)
Stores
LabelledResultsVector as they are calculated, and writes to the file-system.Allows results to be written to a
FeatureCSVWriter, possibly adding further processing.Creates a new instance of
LabelledResultsCSVWriter.Like a
ResultsVector but additionally contains labels to describe the calculated results.Like a
ResultsVectorWithThumbnail but additionally contains labels to describe the
calculated results.Like
WithConfidence but additionally adds a label.Writes a unique ID (successive integer IDs) for each elements's voxels into a channel, and 0 for
background.
Calculates labels for a given input (and index).
Resizes with an interpolator that uses Lanczos resampling as implemented in
Imglib2.
Utility functions for pluralizing words in strings.
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
A command-line interface used for launching experiments.
Specifies a configuration of the launcher for a particular application.
Lazily delays evaluating items until when they are first retrieved.
Returns true iff
valueFirst is less than valueSecond.A relation
double1 < double2.Returns true iff
valueFirst is less than or equal to valueSecond.A relation
double1 <= double2.Calculates a level (a threshold-value) from a histogram.
Creates a channel with a level calculated for each object using various methods.
Creates a channel with different threshold-levels for each object, calculating the level only
from the histogram of the particular object.
Calculates a threshold-level for each object collectively based on other objects
Represents the result of a level operation, containing the level value, object mask, and
histogram.
A collection of
LevelResult objects that can be iterated over and searched.Factory for creating
LevelResultCollection objects.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.Resizes with an interpolator that uses linear interpolation as implemented
in Imglib2.
Fits a set of points to an ellipse using a linear least squares method.
Fits an ellipsoid to points using a linear least squares approach
Base class for linear least squares fitting using the normal equation method.
Represents a line segment in 3D space as a Mark.
Factory for creating a
List of beans.A list of items with an associated thumbnail-batch.
Combines a chain of many exceptions into a single exception, searching for an ultimate cause and
incorporating the messages from the chain into a single unified message.
Caches a small number of slices around which we wish to work, so the memory is efficiently
accessed.
A logging-mechanism for both messages and errors.
Fixture to create a
Logger that don't output anything.The destination(s) to which log-messages are sent.
A cache that discards items that haven't being used recently or frequently.
A tree map that creates a new item, if it doesn't already exist upon a get operation.
Like a
MapCreate but with an associated counter for each element.Abstract base class representing a mark in 3D space.
Abstract base class for defining bounds on marks in a marked point process.
An abstract provider for
MarkBounds.An ordered collection of
Marks.An abstract base class for proposing an entire collection (configuration) of marks.
Provides a collection of marks
Factory class for creating conic marks (ellipses and ellipsoids) from points.
A factory for creating Ellipse marks.
A factory for creating Ellipsoid marks.
A bean for evaluating marks using features and energy schemes.
An abstract base class for factories that create Mark objects.
An abstract base class for proposing a selection of a single mark from a collection of marks.
An abstract base class for proposing merges between marks.
Represents a pair of marks, with a source and destination.
A factory for creating PointList marks.
An abstract base class for proposing changes to a mark.
Annotates each image with a mark using a mark proposer and points fitter.
An abstract base class for defining regions associated with marks.
An abstract base class for beans related to marks in MPP (Marked Point Process).
Initialization class for marks-related components in the MPP framework.
Factory for creating
MarksInitialization instances.An abstract base class for proposing splits of a mark into two new marks.
Marks with both the total energy and a breakdown by clique.
A collection of marks with an associated (total) energy.
Converts a confidence-associated
Mark to an equivalent ObjectMask.A factory for creating marks with unique identifiers.
An abstract base class for marks that have a position in 3D space.
Base-class for a conic that has a single radius (circle, sphere etc.)
A channel whose voxel-values are restricted to two states (on and off).
Performs a logical and operation on corresponding voxels in two
Masks.Loads
Mask to compared, converting it into an ObjectMask.Calculates a feature, treating a mask as a single-object on the energy-stack.
Helper routines to create new instances of
Mask.Creates two or three-dimensional
Masks for tests.Creates a
Mask from one or more ObjectMasks.No outputs are produced.
Inverts masks and objects.
Performs a logical or operation on corresponding voxels in two
Masks.Implementation of
MaskProvider that calls a single delegate MaskProvider.Utility functions for reading a
Mask from the file-system.Performs a logical xor (exclusive or) operation on corresponding voxels in two
Masks.Provides an
ObjectCollection by matching objects using a specified ObjectMatcher.An object with associated matches.
Helper class for matching objects based on intersection.
Maybe imposes a file-extension condition, optionally on top of an existing matcher.
Matches paths using a Java-style glob.
Predicates that matches a file-path against a regular expression.
1.
The maximum of the results from a particular feature.
The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Calculates the maximum value in a histogram.
A feature that calculates the maximum value from a list of features.
Creates a maximum intensity projection of a 3D
Channel.Maximum number of voxels on any slice's contour (edge voxels) across all slices.
Maximum number of voxels in the object-mask across all slices.
Converts a
Channel to UnsignedByteBuffer by scaling against the maximum
intensity value that appears in it.Converts a
Channel to UnsignedByteBuffer by scaling against the maximum
intensity value from a corresponding histogram.Creates buffers for performing a Maximum Intensity
Projection.
Maximum-intensity-projection
across
Channels.Creates a new channel by taking the maximum value of corresponding voxels from two input
channels.
Replaces voxel values with a constant value if the constant is greater than the original voxel
value.
The mean of the results from a particular feature.
Calculates the mean value of a histogram.
Arithmetic mean of a list of features
Calculates the mean of a feature applied to each connected component
Applies a 2D mean filter to a channel using ImageJ's
RankFilters.A feature that calculates the geometric mean of a list of features.
Creates buffers for performing a mean-intensity-projection.
Creates a mean intensity projection of a 3D
Channel.Mean-intensity-projection across
Channels.Calculates the mean value in a
Histogram, and raises it to a power.Stores the mean and scale for a distribution.
Creates a new channel that is the mean of three input channels.
Applies a median-filter with square kernel
Calculates the median value in a
Histogram.Applies a 2D median filter to a channel using ImageJ's
RankFilters.Applies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin.
An interface for accessing voxelized mark memos by index.
Logs a message about approximate memory (RAM) usage of the JVM.
A base class for algorithms that merge object-masks.
Functional interface for merging objects.
Evaluates a feature on the merged object created from a pair of objects.
The list of features that can be used in a
PairsTableCalculatorSpecifies which parts of a merged pair to include in calculations.
A graph that stores each object as a vertex, where edges represent a neighborhood relation.
Naive greedy merge strategy when any two neighboring objects are merged if it increases a
feature.
Merges objects if a pair feature value satisfies a condition.
Merges neighboring objects if it results in an increase in the average feature-value calculated
on each single object.
Merges itemwise objects from two collections.
Base class for object-merging strategies that involve calculating a feature.
Expands
MergeBase by optionally imposing a maximum-distance requirement between objects
that are possibly merged.Logs messages (strings) somewhere.
Logs error messages into a
String via StringBuilder.1.
Abstract base class for imposing minima on a channel for watershed segmentation.
Imposes minima on a channel using grayscale reconstruction by erosion.
The minimum of the results from a particular feature.
Calculates the minimum value of a feature applied to both objects in a pair.
The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
Calculates the minimum value in a
Histogram.A feature that calculates the minimum value from a list of features.
Applies a minimum filter to a channel using ImageJ's MinMaxMedian plugin.
Calculates a scale factor to ensure a minimum XY resolution is achieved.
Creates buffers for performing a minimum intensity projection, similarly to
MaxIntensityProjection but calculating the minimum.The minimum and maximum associated with a range of values.
Minimum-intensity-projection across
Channels.Creates a new channel by taking the minimum value of corresponding voxels from two input
channels.
Replaces voxel values with a constant value if the constant is less than the original voxel
value.
A feature that returns the number-of-voxels in an object by using am internal mock-calculation.
Creates a mock-feature which used a mock
CalculationPart under the hoodCalculates the skewness of all the
values in the histogram.
Runs executes sequence of jobs/tasks/whatever monitoring various pieces of information - how many
have run?
Creates a montage of images, by tiling them side-by-side.
A
Stack into which individual images are written, together with the necessary information
on where to write each image.Creates a montage of slices from a stack.
Performs morphological erosion operation on an
ObjectMask or BinaryVoxels.Specifies a certain number of iterations of the morphological operations of dilation and erosion.
Applies an ImageJ (2D) morphological operation to each slice
Base class for performing morphological operations on
BinaryVoxels.Applies the MSER algorithm from imglib2
An input to an experiment that combines a particular
Stack with other types of entities.Manages input for
MultiInput objects, combining various input sources.A sub-item of a
MultiInput that manages a map of objects.Outputs are enabled if they are contained in both of two
MultiLevelOutputEnableds.Base class for operations that combines two
MultiLevelOutputEnableds.The complement of an existing
MultiLevelOutputEnabled where disabled outputs are enabled,
and vice-versa.Outputs are enabled if they are contained in either of two
MultiLevelOutputEnableds.Whether an output is enabled or not in a context of hierarchy of different rules for outputting.
Like
RecordedOutputs but accepts two levels, first and second, like in a MultiLevelRecordedOutputs.A name that that uniquely identifies an entity, and is composed of two parts.
Creates
MultiName.Allows comparison of an annotation with multiple other entities.
A
Generator that creates multiple different file-types.Logs messages to multiple other loggers.
A feature that multiplies the results of multiple features together.
A feature that multiplies the result of another feature by a constant value.
Multiplies each voxel value in a channel by a constant value.
Creates a new channel by multiplying corresponding voxels from two input channels.
An
ObjectMask that exists at multiple scales.A bean with an associated textual name.
Associates a name with a
Channel.A collection of
Channels each with an associated unique-name.An image viewed as a set of channels, each with a unique name.
Parent for all the
NamedChannels classesExposes one or more instances of a
NamedChannelsMap as a single aggregated NamedChannelsMap.Provides a set of channels as an input, with each channel having a name.
One part of a
NamedChannelsInput that can be combined with others.A collection of
Channels, each identified by a unique name and a time-index.An exception that occurs when a feature fails to successfully calculate.
A
FeatureCalculatorMulti with associated feature-names.Stores
Features, each with an associated name, with list-like access and map-like access.Creates a
NamedFeatureStore.A file with an associated unique name.
Implementation 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.A path and associated name.
A collection of elements, each with an associated name.
Exposes elements in a
NamedProvider as a different type.Combines one more
NamedProviders into a unitary NamedProvider.When a get operation fails with a
NamedProvider.Outputs entities from a
NamedProvider into a directory using the names of each entity for
a corresponding generated file.A
NamedProvider, in which items can also be added.A set of image-stacks each with a name.
Outputs a named-set of stacks, performing appropriate checks on what is enabled or not.
Supplies a
NamedProvider of Stacks.Like
NamedStacks but enforces a condition that all stacks must have the same dimensions.A pair combining a name and a value.
Builds a mapping from names to values, given
NameValue instances.Resizes with an interpolator that uses nearest neighbor
interpolation as implemented in Imglib2.
Creates a graph where each vertex represents an
ObjectMask and edges between indicate
that two objects neighbor each other.A region in proximity to a voxel, encompassing this voxel as well as others.
A condition to determine if two objects are potential neighbors and candidates for merging.
Creates either a big voxel-neighborhood or a small voxel-neighborhood.
A predicate on whether a neighbor satisfies a condition in relation to a particular point that it
neighbors.
An implementation of
Interpolator that performs no interpolation.No outputs are enabled.
All outputs are disabled except particular ones.
Indicates that a collection must have at least one item.
Non image file-formats that are read or writeten to the filesystem, each with an associated
extension.
The bean-field should have a value
>= 0.Normalizes the voxel intensity by dividing it by a constant value.
This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
Corrects a channel in the following way
Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
The range of two feature values (i.e. max - min), divided by their mean.
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
Fake shared-state to use to indicate none exists (for type safety)
Returns true if two values are not equal, and false otherwise.
A negative-result when an object is not found at a particular location.
Filters objects to keep only those which are NOT in the container.
Keeps only objects that are not adjacent to the scene-border (i.e. have a bounding-box on the
very edge of the image)
When initialization should occur of a bean, but no parameters (containing data) are required.
Does nothing with with any messages logged.
A base class for beans that require initialization but the initializations needs no parameters.
The number of channels in an image.
The number of channels in an image-stack.
Number of unique values in histogram.
The number of frames in an image.
A feature that calculates the number of objects intersecting with the input object.
1.
Calculates the number of voxels on the object that have a neighbor.
Calculates the number of objects in a
FeatureInputObjectCollection.How many pixels are removed after a morphological closing operation on the object-mask.
The number of resolution-levels in an image in a file.
The number of series in an image-file.
Converts a number to a strings of constant width by padding with leading zeros.
A scheme for counting the touching voxels by intersection of object-masks
A scheme for counting touching voxels.
Calculates the number of voxels in a single object.
Calculates the number of voxels at the border of an object.
Calculates a feature for a set of objects using this stack as an energy-stack, and aggregates.
Writes an object-mask as a mask (i.e. as a raster image)
A collection of
ObjectMasks.Creates
ObjectCollection using various utility and helper methods.Base class for beans that implement
Provider to provide an ObjectCollection.Base class for object collection providers that apply a filter to the objects.
Base class for providers that apply morphological operations to an
ObjectCollection.Implementation of
ObjectCollectionProvider that calls a single delegate
Provider<ObjectCollection>.An abstract base class for object collection providers that use a feature evaluator.
Reads an
ObjectCollection from the filesystemLike an
ObjectCollection but each object has associated properties.Centralized point to access a
Generator which writes an ObjectCollection to the
file-system.A means of extracting attributes associated with a particular object (e.g. color, ID) when
drawing
Base class for filtering an
ObjectCollection to remove objects according to a criteria.A filter that combines other filters (in a list)
Uses a predicate to make a decision whether to keep objects or not.
An independent object-filter that uses a relation in its predicate.
An object that can be reduced.
Utility functions for creating one or more
ObjectForReductions.Create an
ObjectMask from a collection of points.Deserializes using Java's Native serialization framework.
Utility class for removing intersecting voxels between objects in a collection.
A localized-mask in an image, expressed as a
BoundingBox, with a corresponding mask sized
to match the bounding-box.Merges one or more
ObjectMasks into a single object.A custom "stream" like class for various functional-programming operations on
ObjectCollectionMatches an object with other objects.
Generator that writes an element to the file-system using the Java
ObjectOutputStream
format.Calculates the standard deviation of distances from surface voxels to the centroid of an
ObjectMask.An
ObjectCollection to be compared against something else.Base class for generators that accept a set of objects as input.
A base class for generators that draw an
ObjectCollection upon a RGBStack.Writes objects as an image with an incrementing unique integer id value for each object.
A way to scale a group of
ObjectMasks, scaling each object independently or collectively.Determines which instance of
ObjectScalingMethod to apply.Creates a
ObjectCollection from the connected-components of a mask or binary-voxels.Writes objects merged together as a mask.
Holds two
ObjectCollections for comparison purposes.A vertex in a merge graph representing an object (and an associated payload).
Creates an assignment between intersecting voxels in two objects.
Like
ObjectAsMaskGenerator but additionally outputs a serialized bounding box.A pair containing an
ObjectMask and its corresponding best-fit Ellipse.Finds the object with the maximum feature-value from a collection.
Finds the object with the maximum feature among a group of matches for each object.
An
ObjectMask with associated key-value properties.Like a
PointTwoDimensionalConsumer but also has a buffer offset.Like a
ScalarTwoDimensionalConsumer but accepts two coordinates of a point and an offset
value.Writes a stack to the filesystem as an OME-TIFF using the Bioformats library.
Writes a stack to the filesystem as an OME-XML using the Bioformats library.
Selects one specific channel from a set of stacks
A base-class for a
StackWriter that writes an image that has either one or three
channels.A
SingleFileTypeGenerator that does not transform an element before generating.Logs messages to a particular location ONLY if debug-mode is enabled.
A model that can be used for inference using the ONNX
Runtime's Java API.
Interpolation using OpenCV for resizing an image.
A model that can be used for inference using OpenCV's DNN
module.
Reads a stack from the file-system using OpenCV.
Writes a stack to the file-system using OpenCV and a specified extension.
An image file that has been opened for reading containing one or more series of image-
Stacks.A
OpenedImageFile where the image is formed from more than one file on the file-system.A set of named
Channels available from an OpenedImageFile.Context objects for general operations that allow for logging and recording execution time.
Generic checked exception that can be thrown when a particular operation fails.
Generic runtime exception that can be thrown when a particular operation fails.
Stores objects as operations in a map, implementing the
MultiInputSubMap interface.Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must
always have a non-null value.
Creates a
Comparator that can work with Optionals.Utility functions to create
Optional from flags.A simple container expressing a value and an associationed optional name.
An interface for proposing a position in 3D space.
Additional utility functions for
Optional and exceptions.Outputs the logical operation or voxelwise on both masks, modifying {mask} with the
result.
Applies multiples filter with logical OR i.e. an object must pass any one of the filter steps to
remain.
An interface for providing an ordered list of features.
The orientation (direction) in
2D or 3D Euclidean space.
A simple angular orientation the 2D plane, relative to the x-axis.
An orientation using three angle parameters for the rotation.
An orientation in axis-angle representation.
Changes orientation of an image in the XY plane.
An abstract base class for proposing orientations for marks.
Reads the image-orientation from EXIF metadata, if specified in an image-file.
Orients an object by rotating anti-clockwise with an explicit
RotationMatrix.Performs auto-thresholding using Otsu's method.
Similar to Otsu, but weighs the variances differently of background and foreground.
Draws the outline of each object-mask.
Sets voxels on the outline of an object to be on and otherwise off.
A base class for kernels that find the outline of an
ObjectMask.Base class for features that apply a kernel to the outline of an object.
Outputs the outline of an object-mask, but only for voxels on the exterior which neighbor a
binary-mask.
Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it
centered in a window of a certain size.
Arguments that can further specify an experiment's output in addition to its bean
specification.
When an output-directory already exists.
Whether a particular output, identified by a textual name, is enabled or not.
Additional output-names to enable or disable from an existing set of output-enabled rules.
A specific set of first-level outputs are enabled, to which more can be added.
Bean that specifies an implementation of
MultiLevelOutputEnabled.Base class for an
OutputEnabledRules that specifies particular output-names for first and
second levels.An
Experiment that produces output files, as defined by a OutputManager.SelectParam<Path> factory for outputs.Specifies a table of feature-calculations on objects.
Responsible for making decisions on where output goes and what form it takes.
A fixture that implements a basic implementation of a
OutputManager.Base class for an approach to generate a filename for an output.
A particular naming pattern files follow when outputted.
A
OutputPattern that outputs a file-name with a trailing integer index.A
OutputPattern that outputs a file-name with a trailing string index.Arguments influencing into which directory outputs are written, and how identifiers are
expressed.
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.Creates and starts an output-seqience with a particular generator and context.
A sequence of outputs that use the same generator, where each output increments an index by one
in the filename.
A sequence of outputs that use the same generator with non-incrementing indexes for each output.
Creates output-sequences of different kinds for writing stacks to a directory.
Like
OutputterChecked but exceptions are reported in a ErrorReporter.A particular directory on the filesystem in which outputting can occur.
A fixture that implements a basic implementation of a
OutputterChecked.Utility class for creating Outputter instances for testing purposes.
The directory and prefix an outputter writes to.
Settings and user-arguments for writing files.
When an output could not be successfully written to the file-system.
Settings for how to write output, including default writers.
How to handle voxels whose neighbors are outside the scene.
Calculates a voxel score based on whether the voxel intensity is outside a specified range.
An object-mask that is founded to overlap with another during labelling.
Pairs an
ObjectMask in one set with an ObjectMask in another, if deemed to
overlap sufficiently.Expresses the number of intersecting pixels between two objects as a ratio to a denominator.
Calculates the overlap ratio between two objects relative to the size of the first object.
Overlap ratio to the maximum number of pixels
Calculates the overlap ratio between two objects relative to the size of the merged object.
Calculates the overlap ratio between two objects relative to the size of the second object.
Utility class for calculating overlap between voxelized marks.
Overlays one image on the other.
An entity that will eventually be drawn on top of an image.
A collection of
Overlay objects.Factory for creating
OverlayCollections from marks and retrieving marks from OverlayCollections.An implementation of
Overlay that draws an ObjectMask on an image.Padding (whitespace of certain extent) placed around an object in XY direction and in Z
direction.
Evaluates the object as a pair-feature together with the binary-mask from the shared objects.
Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of
single-object features and pair features.
A feature-session to evaluate pairs of objects.
Represents a pair of VoxelizedMarkMemo objects, with a defined source and destination.
Executes jobs in parallel across cores on the system.
Parameters for executing a task, when the log etc. are still bound to the experiment.
Retrieves a parameter as stored in a
Dictionary in SharedObjects.Parses command-line arguments and runs an experiment.
A collection of
FileDetails objects with methods to query their properties.Converts file-paths between relative and absolute.
Calculates the "difference" between a path and a base.
When an error occurs calculating the difference between two file-paths.
Utility class for deriving paths from a generator.
Helper routines for performing operations on
Paths.Base classes for methods to determine an output directory and associated file prefix.
A file-path-resolver that adds additional methods that perform the same function but output a
relative-path rather than an absolute path after fully resolving paths
Context parameters provided to a link
PathPrefixer.Thrown when unable to successfully determine a prefix for a path.
Matches a regex against incoming file-paths to form a prefix for output
Utility interface to supply a
Path or throw a DerivePathException.Finds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the
name.
Calculates a payload value for an
ObjectMask.Allows all output-names to be outputted in both first and second level.
All outputs are enabled except particular ones.
Imposes a permutation on some property of a bean.
Creates instances of
PermutationAssigner.Permutes some changes over an
ObjectCollectionProvider and collects all the results in an
ObjectCollectionApplies a
PermuteProperty to a bean to create new duplicated beans each with different
permuted values.Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
Permutes one or more properties of a Feature, so as to create a set of Features
Creates permutations of a feature by modifying a particular property of it in different ways.
Permutes a property on a feature with a sequence of integers.
Permutes a feature by applying first and second order statistical operations.
Functional interface for creating first and second order statistical operations.
Permutes a feature by embedding it in a
GaussianCumulative score.Changes properties of an
AnchorBean to one of a range of possible values.Assigns each element from a set of doubles to a particular property of a bean.
Base class for assigning a sequence of numbers to a particular property of a bean.
Assigns an arithmetic sequence of doubles, derived by diving an integer sequence by a divider.
An arithmetic sequence of integers, each directly assigned to a property during permutation.
Assigns each element from a set of strings to a particular property of a bean.
Permutes a feature by embedding it in a
ZScore.Writes a PNG image using ImageJ.
The headers found in a PNG file.
For testing all
StackWriters that create PNGs.A two-dimensional point of double values.
A two-dimensional point of float values.
A two-dimensional point of int values.
A three-dimensional point of double values.
A three-dimensional point of float values.
A three-dimensional point of int values.
Utility class to ensure a point has values contained inside image-dimensions.
Conversion utilities between points with different types and dimensionalities.
A a list of 3D points.
A base class for marks that consist of a list of 3D points.
A factory for creating PointList objects from various types of point collections.
Tracks the range experienced by points in the X, Y and Z dimensions.
An abstract base class for beans that work with points and require initialization.
Abstract base class for fitting a mark (e.g., an ellipsoid) to a set of points.
Exception thrown when an error occurs during the point fitting process.
A bean for fitting points to a mark using a specified points fitter.
Extracts list of points from a
Mask.Derives collections of points from an
ObjectMask or its contour.Creates a
MarkCollection of point marks from an ObjectCollection.Initialization class for points-related components in the MPP framework.
Checks if two or more points fulfill certain neighbor relations to each other.
An abstract base class for proposing a list of points based on a given point and mark.
Like a
IntConsumer but accepts two coordinates of a point as scalar arguments.Represents a polygon in 2D space as a Mark.
Represents a polygon curve in 3D space as a Mark.
Helps populates a
NamedProviderStore from the contents of a Define.The choices of text that may describe the position of an entity along a particular axis.
A constant set of text strings used to indicate particular choices.
An abstract base class for proposing positions.
The bean-field should have a value
> 0.Loading and printing predefined-tasks.
Projects a
VoxelsPredicate to a corner in a larger global spaceLike
ProcessBufferBinary but returns a boolean.Implementation of
VoxelsPredicate for a particular Voxels.Processes a
KernelPointCursor and evaluates a predicate on the current position.Like
Predicate but takes two bytes as argument.Prepends a specific color to the list created by another
ColorScheme.Prepends a string to the custom-name of each feature in a list.
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.
Utility class for converting paths to a more user-friendly representation.
A bean that provides a collection of primitive-types or
Strings.Type conversion between primitive data types.
Calculates the eccentricity of the Principal Axes (as defined by Image Moments).
The length of a principal-axis (as defined by Image Moments).
An element from orientation of a principal-axis (as defined by Image Moments).
A vertex with a priority attached, and a boolean flag as to whether it can be merged or not
Creates a priority between two vertices for object merging.
Implements a priority queue based upon a range of values from 0 to maxValue.
Processes a 3D point like
ProcessPoint but also retrieves two Buffer for
the current z-slice.Processes a 3D point like
ProcessPoint but also retrieves both one VoxelBuffer for the current z-slice and one Buffer for the current z-slice.Processes two buffers for each z-slice jointly, without any offset or point.
Processes a 3D point like
ProcessPoint but also retrieves three buffers for the
current z-slice.Processes a 3D point like
ProcessPoint but also retrieves a buffer for the current
z-slice.Processes a point which has been translated (changed) relative to another point - and includes
global coordinates and includes an object-mask buffer.
Called when a single line is read by a CSV-reader to determine how the entry is further
processed.
Processes a
KernelPointCursor which includes a Point3i.Processes a 3D point.
Processes a
Point3i also including an index.Processes two bytes.
Processes a 3D point like
ProcessPoint but also retrieves two VoxelBuffers
for the current z-slice.Processes a 3D point like
ProcessVoxelBufferBinary but rather has one VoxelBuffer
and one buffer, and also exposes a Point3i.Processes two voxel-buffers for each z-slice jointly, without any offset or point.
Processes a 3D point like
ProcessPoint but also retrieves a VoxelBuffer for the
current z-slice.Processes a 3D point like
ProcessVoxelBufferUnary but also exposes a Point3i.Processes a point that is an neighbor of another.
Processes a point that is a neighbor of another - includes global (absolute) coordinates for this
point.
Like
ProcessVoxelNeighborAbsolute but additionally includes a SlidingBuffer.Creates
ProcessVoxelNeighbor to match certain circumstances.A buffer to which slices may be added to form a projection.
An aggregator that calculates the aggregation of every voxel across successive channels
via a
ProjectableBuffer.Base class for projections that map a 3D voxel-buffer to a 2D voxel-buffer.
An exception thrown when a proposal could not be made for an abnormal reason.
An abstract base class for proposer beans in the MPP (Marked Point Process) framework.
Context for proposing operations in the MPP framework.
An exception thrown when something goes wrong in a Proposer.
A class (usually an
AnchorBean) that creates or otherwise supplies another object.Provides a stack-representation of an entity.
Base class for inputs which somehow eventually send up providing stacks, with or without names.
If provisioning an object fails.
Solves a Quadratic Equation by
finding non-complex roots.
Roots (solution) of a quadratic equation.
A quantile of the results from a particular feature.
Calculates the threshold value from a quantile of a histogram.
Calculates a specified quantile value from a
Histogram.Calculates the median of a feature applied to each connected component
Calculates the quantile of a feature applied to each connected component
Converts a
Channel to UnsignedByteBuffer by scaling against a quantile of
the intensity values that appear in it.Converts a
Channel to UnsignedByteBuffer by scaling against a quantile of
the intensity values from a corresponding histogram.Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel
data range
A method to quickly calculate overlap approximately
An abstract base class for proposing radii in a 3D space.
Utility functions for generating random radii for
ConicBase.An abstract collection of items from which one can randomly sample.
An implementation of a
RandomCollection that uses AddCriteria to determine which
marks to add.Generates random numbers from various distributions.
A bean that defines a type of
RandomNumberGenerator.Implements a random-number generator using the
MersenneTwister algorithm.The range (difference in values) between two quantiles
Calculates the statistical range between two feature values, with optional weighting.
A base class for features that compare a value against a range and return different results based
on the comparison.
A base class for setting the boundaries of a range using constant scalar values.
Writes each object as a binary
Mask in a directory.Transforms an entity to a
Stack and writes it to the file-system.Allows us to call an
RasterGenerator<S> as if it was an RasterGenerator<T> using
an function to connect the two.Delegates a
RasterGeneratorSelectFormat to a SingleFileTypeGenerator<T,
DisplayStack>.Uses a delegate raster-generator and optionally applies a conversions before calling
RasterGeneratorDelegateToRaster.transform(T).A
RasterGenerator that selects an appropriate output-format based upon each generated
image.An experiment that takes (primarily) a series of raster images as an input.
Ratio of first-object to second-object in a pair.
Calculates the ratio of non-mode pixels to total pixels in a
Histogram.Calculates the ratio of prinicpal-axis length using Image Moments.
Calculates the ratio of values in a
Histogram that satisfy a specified threshold
condition.A tuple with three-values, respectively for the X, Y and Z dimensions.
Utility class for reading
ImageLabelAnnotation from a file.An opened-CSV file that is read line-by-line and processed.
Reads a
Dictionary from a file in Java
properties format.Reads various image properties from tags in
Metadata.Options that influence how stack is read in
BioformatsReader.Forces a particular settings, but otherwise uses settings from a delegate
Reads
Resolution from an XML file associated an image.Recorded execution-times for operations.
A particular type of operation that has been recorded (en aggregate).
Outputs recorded from
RecordOutputNamesForWriter.Rules to determine what outputting occurs, together with maybe an entity that records the
output-names that are used when writing / querying.
A counter that also records outputs in a message-log and CSV file.
Two writers that record any output-names that are passed as arguments.
Generates a nice string representation of an Exception and its causes according to certain rules.
Reduces the number or spatial-extent of elements by favoring higher-confidence elements over
lower-confidence elements.
Reduces the number or spatial-extent of elements by favouring higher-confidence elements over
lower-confidence elements.
Calculates the aggregate of a feature applied to both the first and second objects in a
FeatureInputPairObjects.Combines a
PriorityQueue (ordering by highest confidence) and a graph-structure
indicating which objects overlap with each other.Calculates the aggregate of the ratio of
first:second and second
:first for a FeatureInputPairObjectsThe result of a reduction operation.
Uses another feature to calculate the value.
Provides a channel by referencing it from a a set of named-channels.
A provider that references an existing
Histogram by its identifier.A provider that references an existing
Mask by its identifier.An
ObjectCollectionProvider that references an existing ObjectCollection by its
identifier.Retrieves an existing stack.
Provides a
MarkCollection by referencing it from the initialization context using an ID.A
PointsFitter that references another PointsFitter by its ID.Creates reference (i.e.
Returns a object-collection by name if it exists, or else calls
objectsElse if it doesn't
exist.Returns an existing marks-collection or an empty set if it doesn't exist
A base class for implementations of
FeatureListProvider that may reference features
created elsewhere.Reflects points in each axes if all points are within a certain distance from it
The regular-expression to use for matching groups.
Matches a Java-style regular expression against the string.
Maps integer IDs to sub-regions in the map.
A singleton class providing a default RegionMap.
Abstract class representing membership of regions using a bit-flag system.
A RegionMembership implementation that uses an AND operation to check membership.
A
RegionMembership implementation that uses an OR operation to check membership.Utility class for managing 8-bit region membership.
A wrapper for
RegionMembership that includes pre-calculated flags and a region ID.Utility class for registering the Bean-factories that are found in anchor-bean (or any other).
Similar to
RegisterBeanFactories but registers additional feature-related bean-factories.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.
Rejects voxels with intensity less than a specified minimum, otherwise calculates a score using
another
VoxelScore.Rejects a set of objects, if any object is not fully connected (pixels form two or more separate
connected components)
Base class that specifies a relation between two
doubles.Defines a constant threshold, and a relation to it.
A base class specifying a threshold and a relation to it.
Matches each object with others, and keeps only those where a relation holds true for all matches
(in terms of features)
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.
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
Splits an identifier into elements by the directory separator, and removes the final element.
Intersecting objects are removed if they have sufficient overlap.
Considers all possible pairs of objects in a provider, and removes those that touch the border.
Removes any whitespace characters from the path
Duplicates a
ColorList produced by another ColorScheme a certain number of times.Repeats a binary segmentation operation for a specified number of iterations.
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing
mask
Generates a file-path by replacing all occurrences of a string-pattern with another
Replaces infinite values in a feature's result with a specified replacement value.
Indicates and provides a mechanism that the
InputManager can be replaced.Replaces NaN (Not a Number) values in a feature's result with a specified replacement value.
Indicates and provides a mechanism that the
OutputManager can be replaced.Replaces a property (an XML element of attribute) on a bean before loading it.
Different strategies on associating a
FeatureCalculationInput with a particular
input.Indicates and provides a mechanism that the
Task can be replaced.Calculates the underlying feature, but replaces the result with a constant if it is an "unusual"
value.
A predicate on whether all necessary arguments exist for some purpose.
Require that debug-mode has been enabled.
A calculation that be invalidated (resetted), removing any existing cached value.
The resolution of an image.
Reads and writes a metadata XML file specifying the image-resolution.
Provides a pre-created
Resolution instance for use in tests.A bound resolved into pixel units.
Like a
CalculationPart but has been resolved against a cache to reuse any existing
identical instance.A
CalculationPartMap that has been resolved against a cache.More advanced implementation of
Path.resolve(java.nio.file.Path).Accesses resource-files associated with this application.
A vector of results of applying a feature-calculations to many entities.
A list of elements of type
ResultsVector.Utility class for testing ResultsVector objects.
A results-vector with an optional thumbnail associated with it.
Always re-use an existing
SessionInputSequential, invalidating it each time a new call
occurs.Constants for referring to the channels in a RGB-stack or RGBA-stack.
A color encoded in RGB color space.
A bean describing a color in the RGB
color space.
Converts a set of channels to a single RGB-stack if the channel-names match, otherwise uses
fallback.A stack with exactly three channels, respectively for red, green and blue
colors.
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.
Defines a root path.
A collection of root-paths indexed by their name.
A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
Creates instances of
RotatableBoundingBox.Rotates an image to match any EXIF orientation information, if it exists.
A matrix that performs a rotation in
Euclidean space.
Labels for each row of feature-results in the outputted CSV row.
Bases class for implementations of R-Trees that store objects with associated geometry.
Mutable class that allows for incrementing jointly sum and count variables, so as to eventually
calculate the mean.
A collection of
RunningSum where an operation is executed on all objects in the
collection.Like a
RunningSum but also remembers the mean and max across all the added
values.Wraps a
RunningSum with an additional variable, indicating the total number of parent
operations.A running sum for tracking points separately in each dimension.
Access previously saved-files in resources.
An abstract base class for proposing scalar values.
Like a
IntConsumer but accepts three coordinates of a point as scalar arguments.Like a
IntConsumer but accepts two coordinates of a point as scalar arguments.Scales all the objects in the collection by a particular scale-factor.
A stack that can be used as a background (and maybe scaled).
Scales the size of a
Voxels<FloatBuffer> and then thresholds it.Scales by compressing a certain range of values into the 8-bit signal.
Scales by compressing a certain range of values into the 8-bit signal
Converts a channel to unsigned byte format, scaling the values based on the original voxel type.
Calculating a scaling-factor from dimensions.
A list of elements, with an
ObjectMask representation, that have been scaled.What to scale X and Y dimensions by.
Like
ScaleFactor but only allows integer scaling-factors in each dimension.Base class for tasks whose primary aim is to scale (resize) an image.
Creates a scaled copy of images, ensuring all images have identical output size.
Creates a scaled copy of images, treating each image independently, and without any padding or
alignment.
Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
Scales different types of entities with a
ScaleFactor.Create a thumbnail by scales an image to a particular size.
Scales the channel in the X and Y dimensions.
Scales the mask in XY dimensions, but not in Z dimension.
Scales the X and Y coordinates of marks in a
MarkCollection using a ScaleCalculator.Creates a channel by scoring objects based on a feature calculation.
Assigns a score (a value indicating how probable something is) to each voxel
Given a monotonically
increasing function of an integer, determine the input value that provides an output value as
close to
target as possible.The function that calculates the output value for a particular input
int.Searches a directory for files whose paths match a particular predicate.
Evaluates a feature on the second object in a pair of objects.
Performs some kind of segmentation on an image.
When a segmentation cannot successfully complete.
Applies a
BinarySegmentation algorithm to derive a mask from a channelSegments a channel into objects using a specified segmentation algorithm.
Performs segmentation of a channel using each object in the upstream collection as a mask.
A base class for algorithms to segment a channel into one or more objects.
Implementation of
SegmentChannelIntoObjects that calls a single delegate SegmentChannelIntoObjects.The background to a segmentation.
Objects that are a result of an instance-segmentation.
Exposes a particular set of segmented-objects at a particular scale.
Using a model-pool, performs instance segmentation on an image producing zero, one or more
objects per image.
Performs instance-segmentation using the ONNX Runtime and an
.onnx model file.Performs instance-segmentation using OpenCV's DNN module and a TensorFlow
.pb SavedModel file.Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D
segmentation.
Segments a stack into objects.
A base class for algorithms to segment a stack into one or more objects - using a pool of models
A
SegmentStackIntoObjectsScaleDecode that scales the input image, before performing
inference, and then decodes the output.Takes each object one-by-one from
objectsSource, and finds matching seeds from
objectsSeedsDifferent methods of selecting an object
T that is used as a parameter for an experiment.Creates an appropriate
SelectParam based upon the options passed to the command-line.Performs a sequence of succesive segmentations
A sequence of integers.
Executes jobs sequentially, without any parallelism.
Calculates features with successively different inputs, without caching any results from one
input to the next.
A generator that writes binary serialized files to the file-system.
A feature-input that will be used in a
SequentialSessionWhen a set operation fails for a particular key.
Calculates the shape regularity of the center slice of an
ObjectMask.Calculates the shape regularity of the maximum intensity projection of an
ObjectMask.A group of features made available to other features to reference.
A subset of features from
SharedFeatures that share a common feature input-type.Objects shared between different components.
Manages filtered image output with shared state across multiple images.
Shared-state that remembers converted inputs for corresponding unconverted inputs.
Shared-state for instance segmentation.
Shared state for writing selected slice information to a CSV file.
Creates a shell around an
ObjectMask by applying morphological operations.Randomizes the order of colors in a list created by another
ColorScheme.Randomly shuffles the order of the inputs.
Like
Shuffle if requested in the InputContextParameters otherwise makes no change
to the inputs.A 16-bit voxel data-type representing signed-short numbers.
Base class for voxel-data-types that are signed and integral.
Deletes any annotation when it is represented by a single file.
A name with only one part, and is always unique.
A simple container expressing a name-value pair.
A constant filename that is identical to the output-name plus extension.
A single
Stack arranged as-is.A score that is calculated on a single channel only.
For an image with a single channel
An index that always uses the same single color
Provides a single file only.
A base class for inputs that refer to a single file.
A
Generator that eventually writes only a single file to the filesystem.Allows us to call an
SingleFileTypeGenerator<V,S> as if it was an
SingleFileTypeGenerator<T,S> using an function to connect the two.Outputs are enabled if they are contained in both of two
SingleLevelOutputEnabled.Base class for a
SingleLevelOutputEnabled that combines two existing such classes.Outputs are enabled if they are contained in a set.
The complement of an existing
SingleLevelOutputEnabled where disabled outputs are
enabled, and vice-versa.Outputs are enabled if they are contained in either of two
SingleLevelOutputEnabled.An interface for any class that defines whether a top-level output is enabled.
Provides (maybe) a single mark
A base class for implementations of
AnnotatorStrategy where a single unique path exists
for every annotation.Base class for exporting features, where features are calculated per-image using a
NamedFeatureStore.A feature table calculator for single objects.
Remembers the different sizes among the files
Maps a
Path to a particular image-size and orientation-change.The size of an entity in the X and Y dimensions.
Calculates the skewness of all the values in
the histogram.
Indicates that this particular bean-field should be ignored during (recursive) initialization.
Extracts a specific slice from a collection of 3D objects.
A container with voxel-buffers for each z-slice.
Segmenting a z-
Stack slice-by-slice.A slice thresholder that applies thresholding within a mask region.
A slice thresholder that applies thresholding to the entire image without using a mask.
An index that places a particular z-slice in local context.
3x3 Sobel Filter
Sorts the input-items in alphabetical order of their input-name.
Creates a new object-collection with objects sorted by a derived feature-value (in ascending
order)
Splits a collection of elements into spatially separate clusters.
Units to describe spatial quantities.
Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
Selects a specific set of channels from stacks, each identified by a stack-name and channel index
A feature based on one specific principal-axis as identified by image moments.
Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
Only specific outputs, identified by a textual name, are enabled.
A base class for features that operate on a specific channel from the energy stack.
A specific list of paths which form the input.
Specifies dimensions explicitly via bean properties.
Specifies each axis-component of a vector in a particular direction.
Represents a 3D sphere mark.
Splits objects in a collection based on intersections with another set of objects.
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn"
points.
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
A path that has been split into two components: a root and a remainder.
One or more single-channel images that all have the same dimensions.
A list of
BoundingBoxes that indicate where to locate corresponding Stacks on a
unified larger image.Base class for a method that determines positions for
RGBStacks when combined onto a
single plane.Creates stacks of 1 or more channels using
ChannelFixture.Writes a stack to the filesystem.
Common identifiers used for storing particular types of images.
A list of
Channels that are permitted to vary in size.Implementation of
StackProvider that calls a single delegate Provider<Stack>.Combines a
Provider<Stack> with a label.Reads an image-
Stack from the file-system.A
StackReader that supports the correction of orientation as images are read from the
file-system.Whether a stack is RGB or RGBA or neither.
An
InputManager where each file provides one or more
Stacks.Provides a single stack (or a time series of such stacks) as an input
A utility class for testing stack writers by writing stacks and optionally comparing them.
Combines a Stack with a map of other stacks.
Attributes describing stack which may determine which writer is used.
Creates
StackWriteAttributes to describe certain attributes.A combination of attributions describing how to write a particular stack and any suggestions from
the user.
Writes a stack (i.e. raster) to the filesystem.
A base class for a
StackWriter delegates to another StackWriter based on values
of a StackWriteAttributes.Base class for testing various implementations of
StackWriter.The standard-deviation of the results from a particular feature.
Calculates the standard deviation of values in a
Histogram.Creates buffers for projecting the standard-deviation.
Projection of the standard-deviation of voxels values across all inputs.
A
MessageLogger that can be started and stopped, and is aware of this state.Does nothing (i.e. simply ignores) with any messages logged.
Calculates a score based upon the statistical mean and standard deviation.
Statistics to be exported, comprised of name-value pairs.
Calculates the steepest descent direction for voxels in a watershed segmentation.
Supplier of an object for a store.
As a stream can only be used once, this data-structure allows for repeatedly getting streams from
a collection.
A generator that writes the contents of a
String to the file-system as text-file.A bean defining a list of
Strings.Creates a
StringList from a XML element.A bean with a pair of strings, representing a mapping from one string to the other.
A bean defining a set of
Strings.Creates a
StringSet from a XML element.A Trie / Prefix Tree that stores
Strings
efficiently.Outputs a file-name involving a string suffix.
Utility functions for manipualting strings.
A job that has been submitted for execution.
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
A feature that subtracts the result of another feature from a constant value.
Subtracts each voxel value in a channel from a constant value.
Subtracts the mean intensity (of the entire channel or a masked portion thereof) from every
voxel.
Calculates
merged - reduce(first,second) for a FeatureInputPairObjectsSubtract second-object from first-object in a pair.
Creates a new channel by subtracting corresponding voxels of the second channel from the first
channel.
An exception thrown by
ImageSizeSuggestionFactory to indicate a format is invalid or
unknown.Sums the results after calculating a list of
Features.The sum of the results from a particular feature.
Calculates the sum of all values in a
Histogram.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.
A special kind of exception that represents a summary of an existing set of exceptions.
Applies a segmentation procedure followed by non-maximum suppression.
The number of voxel-faces along the surface (the faces of each voxel that touch outside)
The number of voxels on the surface (all voxels on the exterior of the object)
A base class for features that calculate the number of voxels on the surface of an object.
Treats the channel index as if it's time, and vice versa
Switches between two log-reporters depending on whether detailed logging is switched on or not
Encapsulates some kind of processing to be performed on a set of inputs.
Arguments that can further specify an experiment's task in addition to its bean
specification.
Determines
Paths related to tasks.Maintains statistics on the execution of a task (considering jobs in aggregate).
A particular type of task that doesn't share-state between running jobs
An exception thrown when test-data cannot be loaded.
An exception thrown when test-data cannot be loaded.
Loads test data, which is found at some location on the filesystem.
A test loader for image-related operations, providing methods to open and compare images and
object collections.
A utility class for loading and processing object masks in test scenarios.
Logs messages to a text-file.
Utility for writing to a text-file at a particular path, but only if it is enabled.
Maybe creates a
TextFileOutput based upon settings in a OutputterChecked.The size and style of text as it should appear in an image.
From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and
Classification of Heterogeneous Populations of Cell Nuclei
Provides a
Stack by combining up to three channels (red, green, blue) into an RGB image.Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel
if possible.
Thresholds each voxels by comparing against another channel that has per-voxel thresholds
Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
Thresholds voxels to create a binary-voxels using global
thresholding.
Applies automatic thresholding using ImageJ's Auto_Threshold plugin.
Performs global thresholding.
A thresholder that applies a simple intensity threshold and then fills holes in 2D.
Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded
version.
Creates thumbnails for a particular batch of objects that can be calibrated to have similar
properties (identical scale etc.)
Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects.
Creates a thumbnail from a stack.
Writes a stack to the filesystem as a TIFF using the Bioformats library.
Writes a TIFF image using ImageJ.
For testing all
StackWriters that create TIFFs.A higher-level aggregate structure that arranges other
StackArrangers in a tabular
pattern.Tile multiple
StackProviders into a single StackProvider.Tiles a number of
StackProviderWithLabels as a single StackProvider.Derives a human-friendly name for a time-interval.
An ordered collection of
Stacks, each representing a frame in a time-series.Extracts a timestamp from a file-name if it exists.
How to style a time in a file-name.
Converts a channel to unsigned byte format without any scaling.
Converts a channel to unsigned byte format using upper and lower quantile intensities from a
histogram.
Logs messages to the console.
Calculates a scaling-factor to make the source image have identical dimensions as
dimensionsTarget.Converts a
Channel to have a voxel data type of FloatBuffer without scaling.Base class for implementations of
ConvertTo that convert to float buffers.Converts voxel buffers to a
FloatBuffer without scaling any values.Rather than logging to one location, logs to multiple locations (from a list).
Scales to the suggested-size if one is provided, otherwise calls
fallback.Calculates the total count of all entries in a
Histogram.Logs to a text-file created in the output-directory under a particular name.
Logs messages to a text-file create in the output-directory.
Logs to a text file like with
ToTextFile but the
log is ONLY written if a failure occurs in the experiment.A feature that raises the result of another feature to the power of a constant value.
Base class for features that calculate touching with a dilated bounding box intersection.
Converts a
Channel to have a voxel data type of UnsignedByteBuffer (unsigned
8-bit) without scaling.Base class for conversion to unsigned 8-bit.
Base class for implementations of
ConvertTo that convert to unsigned byte buffers.Converts voxel buffers to an unsigned 8-bit buffer without scaling any values.
Converts voxel buffers to an unsigned 8-bit buffer linearly scaling against the maximum
constant value.
Converts a
Channel to have a voxel data type of UnsignedByteBuffer (unsigned
8-bit) scaling from the range of the source data-type.Converts voxel buffers to an unsigned 8-bit buffer scaling against a the minimum and
maximum constant.
Converts voxel buffers to a
UnsignedByteBuffer scaling against the maximum value in each
buffer.Like
ToUnsignedByte but applies scaling, if necessary, to map the original value to
8-bits.Base class for conversion to unsigned 32-bit.
Base class for implementations of
ConvertTo that convert to unsigned int buffers.Converts a
Channel to have a voxel data type of UnsignedShortBuffer.Base class for implementations of
ConvertTo that convert to unsigned short
buffers.Converts voxel buffers to an unsigned 16-bit buffer without scaling any values.
Converts voxel buffers to an unsigned 16-bit buffer, scaling against the maximum value in
each data-type.
Performs preprocessing to transform the element into another type before being written to the
filesystem.
Allows us to call an
SingleFileTypeGenerator<V,S> as if it was an
SingleFileTypeGenerator<T,S> using an function to connect the two.A three-dimensional tuple of double values.
A three-dimensional tuple of float values.
A three-dimensional tuple of int values.
Takes the two channels and creates a NEW third channel whose pixels are a function of the two
channels
An edge that exists in a graph, together with the two vertices that it connects.
A union of two types, either
String or a numeric-value.Like a
UnaryOperator but uses the primitive type int.Base class for
ObjectCollectionProviderUnary that also requires a Channel.A base class for a
ChannelProviderUnary which also uses a binary mask.An abstract base class for creating a channel from an existing channel and a collection of
objects.
A
ChannelProviderUnary which has a scalar value field.Converts from voxelized units to different physical measurements of area / volume / distance.
Checks if a value lies within a range defined by units (a minimum and maximum boundary)
A base class for a value that describes an area measurement on the image.
Base class for methods to specify a distance along a vector in an image.
When a failure occurs converting from one type of units to another.
A base class for a value that describes an area or volume measurement, which can then be
resolved to a number of voxels.
A base class for a value that describes a volume measurement on the image.
Base class for buffers that represent an unsigned-type in the signed-equivalent-type NIO
Buffer.A
UnsignedBuffer that exposes its internal types as int.Wraps a
ByteBuffer but automatically performs conversion to int.Converts a
ByteBuffer encoding a float type to unsigned byte type, as
expected in an Anchor VoxelBuffer.Like
ToUnsignedByte and provides common functionality when converting to an unsigned
byte.Converts a
ByteBuffer encoding unsigned bytes (with interleaving) to
unsigned byte type, as expected in an Anchor VoxelBuffer.Converts a
ByteBuffer encoding unsigned bytes (no interleaving) to
unsigned byte type, as expected in an Anchor VoxelBuffer.Converts data of type unsigned byte to unsigned byte.
Converts data of type unsigned int to unsigned byte.
Converts data of type unsigned short to unsigned byte.
A 8-bit voxel data-type representing unsigned-byte numbers.
Wraps an
IntBuffer but automatically performs conversion to long.Convert to an unsigned int buffer, given an unsigned int source buffer.
A 32-bit voxel data-type representing unsigned-int numbers.
Wraps a
ShortBuffer but automatically performs conversion to int.Convert to an unsigned short buffer, given an signed short source buffer.
Convert to an unsigned short buffer, given an unsigned short source buffer.
A 16-bit voxel data-type representing unsigned-short numbers.
Base class for voxel-data-types that are unsigned and integral.
Exception thrown when an unsupported mark type is encountered.
A two-stage process for checking if two
ObjectMasks should be merged.An interface for managing a set of marks that can be updated.
Exception thrown when an error occurs while updating a mark set.
Converts a
Channel to UnsignedByteBuffer by scaling against lower and upper
quantiles of the intensity values that appear in it.Converts a
Channel to UnsignedByteBuffer by scaling against lower and upper
quantiles of the intensity values from a corresponding histogram.Uses whatever default-manager exists
Calculates the variance of all the values in
the histogram.
Calculates variance efficiently, as successive values are added, using
double to store
sums internally.Calculates variance efficiently, as successive values are added, using
long to store sums
internally.Applies a 2D variance filter to a channel using ImageJ's
RankFilters.A three-dimensional vector of double values.
Creates a list by repeating a defined constant list of very bright colors.
Adds a visualization for all binary-masks and object-collections that are added using a
particular background
Calculates the volume (x, y and z dimensions) of the scene from the dimensions
Volume expressed in cubic meters, or units thereof.
Volume expressed in voxels.
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels.Creating voxel-buffers and arrays of voxel-buffers of various types.
Converts a
Mat to a VoxelBuffer.A parent class for
VoxelBuffer that accepts unsigned-buffers and implements some common
operations.Wraps arrays and buffers of primitive-types into
VoxelBuffer.The type of data that a single voxel represents in an image or related buffer.
Multiplexes between factories for the various
VoxelDataTypes.A voxelized representation of a Mark i.e. a mark turned into voxels.
Factory class for creating
VoxelizedMarkHistogram instances.Memoization of retrieving a
VoxelizedMark from a mark.Factory class for creating
VoxelizedMarkMemo instances.A partition of voxel values by slice.
A factory for creating
VoxelPartition instances.A voxel partition implementation using histograms to represent voxel value distributions.
A factory for creating
VoxelPartition instances that use Histograms as parts.Defines a pattern of voxels in a 3D space.
The physical size of a pixel in a specific dimension.
A box (3-dimensions) with voxel-data.
Allows manipulation of voxel intensities via arithmetic operations.
Creates
VoxelsArithmetic for buffers of different types.Assigns values to some or all voxels.
Creates
VoxelsAssigner for buffers of different types.Converts voxels from one data-type to another.
Converts a channel from one voxel data-type to one of multiple other types.
Calculates a per-voxel score.
Provides methods to read/copy/duplicate regions of voxels.
Creates
VoxelsExtracter corresponding to Voxels of differing data-type.Creates
VoxelsUntyped and provides a singleton location for implementations of VoxelsFactoryTypeBound for different types.A factory for creating voxels with a particular buffer-type.
Implementation of
Voxels whose voxels are of type float.Methods to find or count voxels that satisfy a predicate.
Copies voxels while performing interpolation.
Calls another
VoxelsResizer recording each resize call via a ExecutionTimeRecorder.Creates instances of
VoxelsResizer to match particular circumstances.Resizes with linear
interpolation as implemented in ImageJ.
Performs resizing of
VoxelBuffers using ImgLib2's interpolation.Doesn't do any interpolation, just copies a single value for each voxel.
Resizes
VoxelBuffers using OpenCV's cv2.resize function.Allows retrieval of statistics about voxel values.
Aggregates statistics of a list of
VoxelStatistics as if they were one.Calculates statistics from a
Histogram of voxel intensities.Performs a thresholding
operation on voxels.
Implementation of
Voxels whose voxels are of type unsigned byte (8-bit).Implementation of
Voxels whose voxels are of type unsigned int (32-bit).Implementation of
Voxels whose voxels are of type unsigned short (16-bit).Stores memory buffers representing image voxels, without explicit typing of buffers.
Walks in X, Y and Z directions from a point, test a
NeighborPredicate to determine if a
neighbor satisfies conditions.Walks in X, Y and Z directions from a point, executing a
Runnable if the neighbor
satisfies conditions.Encodes watershed-related information in an integer range.
A 'rainfall' watershed algorithm
Base class for
ObjectCollectionProviders that create objects from a Channel.Wraps an element with a confidence-score.
Base class for
ObjectCollectionProviderUnary that take an optional
objectsContainer bean-field.Base class for
ObjectCollectionProviderUnary classes that require dimensions to be
specified.A base class for applying ImageJ rank filters to channels.
Base class for
ObjectCollectionProviderUnary classes that offer an optional means to
specify dimensions.Avoids grouping of inputs, effectively processing all inputs as one large group.
Avoids including an output-name in the filename.
Wraps an element of type
T to ensure priority is given when the flag gpu==true.A
ChannelProviderUnary with a 'radius' parameter.Base class for a feature that requires input resolution to be calculated.
A base class for operations that use a specified constant value in combination with a feature.
Wraps a BeforeCondition as an UpdatableBefoerCondition
Writes one or more stacks/objects/channels into a directory during testing.
Write data via
ElementWriters to the file system, or creates new sub-directories for
writing data to.Helps create similar error messages among
StackWriters.When writing a stack, an additional file is written to indicate the physical voxel sizes, if this
information is known.
Interface for classes with a method that should be called before every outputting write
operation.
Write data via
ElementWriters to the file system.Writes a string to a text file.
Creates an image that contains text only.
A generator that writes the contents of a XML file to the file-system.
Utility functions for parsing XML files using standard Java APIs.
Writes XML in the form of a
Document to the file-system.Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask}
with the result.
Deserializes an object using the XStream library.
A generator that serialized using the XStream library
and format.
Serializes an object using the XStream library.
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
Calculates the Z-score of a value based on the mean and standard deviation.
Calculates a Z-Score.