Modifier and Type | Class and Description |
---|---|
class |
AnnotationBackground
How to display one or more
Stack s as background during an annotation process. |
class |
AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy>
An
InputManager that provides annotations corresponding to images. |
class |
AnnotatorStrategy
How an input is associated with annotations on the file-system, and how this is presented
visually.
|
Modifier and Type | Class and Description |
---|---|
class |
ComparableSource
A set of elements, loaded from the file-system, to be compared to another set.
|
class |
MultipleComparer
Allows comparison of an annotation with multiple other entities.
|
Modifier and Type | Class and Description |
---|---|
class |
NamedBean<T extends AnchorBean<?>>
A bean with an associated textual name.
|
Modifier and Type | Class and Description |
---|---|
class |
NamedBean<T extends AnchorBean<?>>
A bean with an associated textual name.
|
class |
NullParametersBean<T>
A base class for beans that require initialization but the initializations needs no parameters.
|
Modifier and Type | Method and Description |
---|---|
<T extends AnchorBean<?>> |
AnchorBean.findFieldsOfClass(Class<?> match)
Finds all bean-fields that are instances of a certain class.
|
Modifier and Type | Method and Description |
---|---|
static Optional<Object> |
FieldAccessor.fieldFromBean(AnchorBean<?> bean,
Field field)
Retrieves the value of a
Field from a AnchorBean . |
Modifier and Type | Class and Description |
---|---|
class |
Define
A bean where the definitions of many different
NamedBean s can be specified. |
Modifier and Type | Method and Description |
---|---|
<T extends AnchorBean<?>> |
Define.addAll(List<NamedBean<T>> list)
Adds all the named-beans from source to the current map.
|
<T extends AnchorBean<?>> |
Define.listFor(Class<?> groupingRoot)
Retrieves the list of elements associated with a grouping-root.
|
Modifier and Type | Class and Description |
---|---|
class |
Concatenate
Concatenates a list of adders.
|
class |
DefineAdderBean
Base class for
AnchorBean s that can add items to a Define . |
class |
DefineAdderWithPrefixBean
Like
DefineAdderBean but adds a prefix to the name of beans when adding. |
class |
FromXMLList
Adds a list of Named-Items define in a XML file in the current directory.
|
Modifier and Type | Method and Description |
---|---|
protected void |
DefineAdderWithPrefixBean.addWithName(Define define,
String name,
AnchorBean<?> item)
Add an item to
define with a name being added. |
Modifier and Type | Class and Description |
---|---|
class |
InitializableBean<B,P extends BeanInitialization>
A bean that must be initialized with some parameters before being used.
|
Modifier and Type | Class and Description |
---|---|
class |
PermutedCopyCreator<T extends AnchorBean<T>>
Applies a
PermuteProperty to a bean to create new duplicated beans each with different
permuted values. |
Modifier and Type | Method and Description |
---|---|
void |
PermutationAssigner.assignValue(AnchorBean<?> bean,
Object value)
Assigns
value to one or more properties in bean . |
static PermutationAssigner |
PermutationAssignerFactory.createForSingle(AnchorBean<?> bean,
String propertyPath)
Creates an assigner for one or more properties, as identified by
propertyPath . |
Modifier and Type | Class and Description |
---|---|
class |
PermuteProperty<T>
Changes properties of an
AnchorBean to one of a range of possible values. |
class |
PermutePropertyDoubleSet
Assigns each element from a set of doubles to a particular property of a bean.
|
class |
PermutePropertySequence<T>
Base class for assigning a sequence of numbers to a particular property of a bean.
|
class |
PermutePropertySequenceDouble
Assigns an arithmetic sequence of doubles, derived by diving an integer sequence by a divider.
|
class |
PermutePropertySequenceInteger
An arithmetic sequence of integers, each directly assigned to a property during permutation.
|
class |
PermutePropertyStringSet
Assigns each element from a set of strings to a particular property of a bean.
|
class |
SequenceInteger
A sequence of integers.
|
Modifier and Type | Method and Description |
---|---|
PermutationAssigner |
PermuteProperty.createSetter(AnchorBean<?> bean)
Creates a
PermutationAssigner which allows the particular property to be changed. |
Modifier and Type | Class and Description |
---|---|
class |
DoubleList
A bean defining a list of
Double s. |
class |
DoubleSet
A bean defining a set of
Double s. |
class |
IntegerList
A bean defining a list of
Integer s. |
class |
IntegerSet
A bean defining a set of
Integer s. |
class |
StringList
A bean defining a list of
String s. |
class |
StringSet
A bean defining a set of
String s. |
Modifier and Type | Class and Description |
---|---|
class |
StringMap
|
class |
StringMapItem
A bean with a pair of strings, representing a mapping from one string to the other.
|
Modifier and Type | Class and Description |
---|---|
class |
RGBColorBean
A bean describing a color in the RGB
color space.
|
Modifier and Type | Class and Description |
---|---|
class |
ColorScheme
Creates a sequence of related colors.
|
class |
ColorSchemeUnary
Like
ColorScheme but employs a unary operator on a call to an existing ColorScheme . |
class |
FromList
Specifies a list of colors by a list.
|
class |
FromSingle
A single color repeated to meet the size.
|
class |
HSB
Creates a sequence of colors by varying the hue-component in a HSB color
model.
|
class |
Prepend
Prepends a specific color to the list created by another
ColorScheme . |
class |
Repeat
Duplicates a
ColorList produced by another ColorScheme a certain number of times. |
class |
Shuffle
Randomizes the order of colors in a list created by another
ColorScheme . |
class |
VeryBright
Creates a list by repeating a defined constant list of very bright colors.
|
Modifier and Type | Class and Description |
---|---|
class |
DictionaryBean<T>
Base class for beans that require initialization with
DictionaryInitialization . |
class |
DictionaryProvider
Base class for beans that implement
Provider to provide a Dictionary . |
class |
DictionaryProviderReference
References a particular
Dictionary in shared-object-space. |
Modifier and Type | Class and Description |
---|---|
class |
FilePathBean<T>
Base class for beans that require initialization with
FilePathInitialization . |
class |
RootPath
Defines a root path.
|
Modifier and Type | Class and Description |
---|---|
class |
RandomNumberGeneratorBean
A bean that defines a type of
RandomNumberGenerator . |
Modifier and Type | Class and Description |
---|---|
class |
RegEx
The regular-expression to use for matching groups.
|
class |
RegExList
|
class |
RegExSimple
Matches a Java-style regular expression against the string.
|
Modifier and Type | Class and Description |
---|---|
class |
EqualToBean
A relation
double1 == double2 . |
class |
GreaterThanBean
A relation
double1 > double2 . |
class |
GreaterThanEqualToBean
A relation
double1 >= double2 . |
class |
LessThanBean
A relation
double1 < double2 . |
class |
LessThanEqualToBean
A relation
double1 <= double2 . |
class |
RelationBean
Base class that specifies a relation between two
double s. |
Modifier and Type | Class and Description |
---|---|
class |
RelationToConstant
Defines a constant threshold, and a relation to it.
|
class |
RelationToThreshold
A base class specifying a threshold and a relation to it.
|
Modifier and Type | Class and Description |
---|---|
class |
ReplacePropertyBeanFactory<T extends AnchorBean<T>>
Replaces a property (an XML element of attribute) on a bean before loading it.
|
Modifier and Type | Method and Description |
---|---|
static Path |
BeanPathCalculator.pathFromBean(AnchorBean<?> bean,
String relativePath)
Calculates a path from the current bean.
|
Modifier and Type | Class and Description |
---|---|
class |
Experiment
A base class for a type of task that produces some kind of result of interest.
|
Modifier and Type | Class and Description |
---|---|
class |
ExperimentIdentifier
A method to produce an identifier for an experiment.
|
class |
ExperimentIdentifierAuto
Automatically populates a experiment-name and version number
|
class |
ExperimentIdentifierConstant
Defines constants for name and version of an experiment
|
Modifier and Type | Class and Description |
---|---|
class |
InputOutputExperiment<T extends InputFromManager,S>
An experiment that uses both an
InputManager to specify inputs and a OutputManager to specify outputting. |
class |
OutputExperiment
An
Experiment that produces output files, as defined by a OutputManager . |
Modifier and Type | Class and Description |
---|---|
class |
LoggingDestination
The destination(s) to which log-messages are sent.
|
class |
OnlyIf
Logs messages to a particular location ONLY if debug-mode is enabled.
|
class |
SwitchDetailedLogging
Switches between two log-reporters depending on whether detailed logging is switched on or not
|
class |
ToConsole
Logs messages to the console.
|
class |
ToMultiple
Rather than logging to one location, logs to multiple locations (from a list).
|
class |
ToTextFile
Logs to a text-file created in the output-directory under a particular name.
|
class |
ToTextFileBase
Logs messages to a text-file create in the output-directory.
|
class |
ToTextFileOnlyIfFailure
Logs to a text file like with
ToTextFile but the
log is ONLY written if a failure occurs in the experiment. |
Modifier and Type | Class and Description |
---|---|
class |
DebugDependentProcessor<T extends InputFromManager,S>
Executes different processors depending on whether we are in debug mode or not.
|
class |
JobProcessor<T extends InputFromManager,S>
Base class for a method to apply a task on inputs.
|
class |
ParallelProcessor<T extends InputFromManager,S>
Executes jobs in parallel across cores on the system.
|
class |
SequentialProcessor<T extends InputFromManager,S>
Executes jobs sequentially, without any parallelism.
|
Modifier and Type | Class and Description |
---|---|
class |
RequireArguments
A predicate on whether all necessary arguments exist for some purpose.
|
class |
RequireDebugMode
Require that debug-mode has been enabled.
|
Modifier and Type | Class and Description |
---|---|
class |
Task<T extends InputFromManager,S>
Encapsulates some kind of processing to be performed on a set of inputs.
|
class |
TaskWithoutSharedState<T extends InputFromManager>
A particular type of task that doesn't share-state between running jobs
|
Modifier and Type | Class and Description |
---|---|
class |
Feature<T extends FeatureInput>
Base class for a measurement that calculates a result (double) given input parameters.
|
class |
FeatureRelatedBean<T>
Beans-related to
Feature s, and which require initialization with FeatureRelatedInitialization . |
Modifier and Type | Class and Description |
---|---|
class |
DefinedNamed<T extends FeatureInput>
Specifies features via a list of names and associated with features.
|
class |
DefineSingle<T extends FeatureInput>
Specifies a single feature directly without assigning any custom-naming.
|
class |
FeatureList<T extends FeatureInput>
A list of features with the same input-type.
|
class |
FeatureListProvider<T extends FeatureInput>
Provides a list of
Feature s with identical input-type. |
class |
PrependName
Prepends a string to the custom-name of each feature in a list.
|
class |
ReferencingFeatureListProvider<T extends FeatureInput>
A base class for implementations of
FeatureListProvider that may reference features
created elsewhere. |
Modifier and Type | Class and Description |
---|---|
class |
FeatureBinary<T extends FeatureInput>
A base class for a
Feature that is a binary-function of the results from two other
features. |
class |
FeatureFromList<T extends FeatureInput>
A base class for a
Feature that is a function of the results from a list of other
features. |
class |
FeatureGeneric<T extends FeatureInput>
Base class for features that broadly accept any type of feature-input.
|
class |
FeatureUnary<T extends FeatureInput,S extends FeatureInput>
A feature that contains another feature as a bean-parameter.
|
class |
FeatureUnaryGeneric<T extends FeatureInput>
A
FeatureUnary that accepts any FeatureInput irrespective of type. |
class |
Reference<T extends FeatureInput>
Uses another feature to calculate the value.
|
class |
Sum<T extends FeatureInput>
Sums the results after calculating a list of
Feature s. |
Modifier and Type | Class and Description |
---|---|
class |
FeatureProvider<T extends FeatureInput>
Provides a single
Feature . |
class |
FeatureProviderBean<B,P>
|
class |
FeatureProviderDefine<T extends FeatureInput>
Defines a single
Feature to provide via a bean property. |
class |
FeatureProviderReference
Provides an existing
Feature identified by its name and optionally a feature-list in
which is resides. |
Modifier and Type | Class and Description |
---|---|
class |
FeatureResults
Features that process
ResultsVectorList . |
class |
FeatureResultsStatistic
Base class for an instance of
FeatureResults that calculating a statistic across all
results in the ResultsVectorList for a particular feature-value. |
Modifier and Type | Class and Description |
---|---|
class |
ImageBean<T>
A bean that must be initialized with
ImageInitialization before usage. |
Modifier and Type | Class and Description |
---|---|
class |
ChannelAggregator
A method of aggregating the voxels from many identically-sized
Channel s into one. |
class |
ConvertChannelTo<T>
Creates a
ChannelConverter for converting a channel to a particular type. |
class |
ConvertChannelToWithHistogram<T>
Creates a
ChannelConverterAttached<Histogram, T> for converting a channel to a particular
type, making use of a Histogram . |
Modifier and Type | Class and Description |
---|---|
class |
IntensityQuantiles
Implementation of
StackDisplayer that converts to unsigned-8bit by taking the upper and
lower quantiles of the intensity range. |
class |
StackDisplayer
|
Modifier and Type | Class and Description |
---|---|
class |
ImgLib2Lanczos
Resizes with an interpolator that uses Lanczos resampling as implemented in
Imglib2.
|
class |
ImgLib2Linear
Resizes with an interpolator that uses linear interpolation as implemented
in Imglib2.
|
class |
Interpolator
Defines a particular type of interpolation method that can be used for resizing images.
|
class |
None
An implementation of
Interpolator that performs no interpolation. |
Modifier and Type | Method and Description |
---|---|
<S extends AnchorBean<S>> |
PopulateStoreFromDefine.copyWithoutInitialize(Class<?> defineClass,
NamedProviderStore<S> destination)
Copies objects of a particular class from the define without performing any
initialization.
|
Modifier and Type | Class and Description |
---|---|
class |
ObjectFilter
Base class for filtering an
ObjectCollection to remove objects according to a criteria. |
class |
ObjectMatcher
Matches an object with other objects.
|
Modifier and Type | Class and Description |
---|---|
class |
BeanProviderAsStackBase<T,S>
A provider base-class that as well as providing type
S , also provides a Stack . |
class |
ChannelProvider
|
class |
ChannelProviderBinary
Implementation of
ChannelProvider that calls two ChannelProvider s that
must provide Channel s of the same dimensions. |
class |
ChannelProviderTernary
Implementation of
ChannelProvider that calls three ChannelProvider s that
must provide Channel s of the same dimensions. |
class |
ChannelProviderUnary
Implementation of
ChannelProvider that calls a single delegate ChannelProvider . |
class |
ColorProvider
|
class |
DimensionsProvider
Base class for beans that implement
Provider to provide Dimensions . |
class |
HistogramProvider
|
class |
HistogramProviderUnary
Implementation of
HistogramProvider that calls a single delegate HistogramProvider . |
class |
MaskProvider
|
class |
MaskProviderUnary
Implementation of
MaskProvider that calls a single delegate MaskProvider . |
class |
ObjectCollectionProvider
Base class for beans that implement
Provider to provide an ObjectCollection . |
class |
ObjectCollectionProviderUnary
Implementation of
ObjectCollectionProvider that calls a single delegate Provider<ObjectCollection> . |
Modifier and Type | Class and Description |
---|---|
class |
Arrange
Creates a stack that combines other stacks.
|
class |
StackProvider
|
class |
StackProviderUnary
Implementation of
StackProvider that calls a single delegate Provider<Stack> . |
Modifier and Type | Class and Description |
---|---|
class |
SegmentationBean<T>
Performs some kind of segmentation on an image.
|
Modifier and Type | Class and Description |
---|---|
class |
BinarySegmentation
Performs a segmentation on voxels so that each voxel has an on or off state after
the operation.
|
class |
BinarySegmentationReference
Uses an existing
BinarySegmentation that is located by a unique identifier. |
class |
BinarySegmentationThreshold
Implementation of
BinarySegmentation that performs global
thresholding. |
class |
BinarySegmentationUnary
An implementation of
BinarySegmentation that delegates to one other BinarySegmentation . |
Modifier and Type | Class and Description |
---|---|
class |
SegmentChannelIntoObjects
A base class for algorithms to segment a channel into one or more objects.
|
class |
SegmentChannelIntoObjectsUnary
Implementation of
SegmentChannelIntoObjects that calls a single delegate SegmentChannelIntoObjects . |
Modifier and Type | Class and Description |
---|---|
class |
Padding
Padding (whitespace of certain extent) placed around an object in XY direction and in Z
direction.
|
class |
ScaleCalculator
Calculating a scaling-factor from dimensions.
|
class |
SizeXY
The size of an entity in the X and Y dimensions.
|
Modifier and Type | Class and Description |
---|---|
class |
StackArranger
Base class for a method that determines positions for
RGBStack s when combined onto a
single plane. |
Modifier and Type | Class and Description |
---|---|
class |
Align
Align the bounding-box to the
larger without resizing. |
class |
BoxAligner
Aligns a smaller
BoundingBox to fit inside a larger BoundingBox . |
class |
Grow
Grow the bounding-box to fill
larger as much as possible. |
Modifier and Type | Class and Description |
---|---|
class |
Fill
Montages
Extent s together to completely fill the available space, while preserving aspect
ratio. |
Modifier and Type | Class and Description |
---|---|
class |
Overlay
Overlays one image on the other.
|
Modifier and Type | Class and Description |
---|---|
class |
Cell
Indicates how to arrange one or more
RGBStack s in a cell in a table. |
class |
Tile
A higher-level aggregate structure that arranges other
StackArranger s in a tabular
pattern. |
Modifier and Type | Class and Description |
---|---|
class |
AxisAlignedUnitVector
Creates a
DirectionVector that is a unit-vector along a particular image-axis. |
class |
DirectionVectorBean
A bean that creates a
DirectionVector . |
class |
SpecifyVector
Specifies each axis-component of a vector in a particular direction.
|
Modifier and Type | Class and Description |
---|---|
class |
CalculateLevelUnary
Implementation of
CalculateLevel that calls a single delegate CalculateLevel . |
class |
Thresholder
Thresholds voxels to create a binary-voxels using global
thresholding.
|
class |
ThresholderGlobal
Performs global thresholding.
|
Modifier and Type | Class and Description |
---|---|
class |
BinaryNotOffVoxels
Selects voxels that are not off voxels.
|
class |
BinaryNotOnVoxels
Selects voxels that are not on voxels.
|
class |
BinaryOffVoxels
Selects only the off voxels.
|
class |
BinaryOnVoxels
Selects only the on pixels.
|
class |
BinaryVoxelsBase
A base class for implementations of
RelationToThreshold where the threshold is derived
from a BinaryValuesInt . |
Modifier and Type | Class and Description |
---|---|
class |
DistancePhysical
Implementation of
UnitValueDistance that specifies a value in physical units, as
described by particular recognized strings. |
class |
DistanceVoxels
Implementation of
UnitValueDistance that specifies a value in voxels, ignoring any
physical image resolution. |
class |
UnitValueDistance
Base class for methods to specify a distance along a vector in an image.
|
Modifier and Type | Class and Description |
---|---|
class |
UnitValueExtent
A base class for a value that describes an area or volume measurement, which can then be
resolved to a number of voxels.
|
Modifier and Type | Class and Description |
---|---|
class |
AreaPhysical
Area expressed in square meters, or units thereof.
|
class |
AreaPixels
Area expressed in pixels.
|
class |
UnitValueArea
A base class for a value that describes an area measurement on the image.
|
Modifier and Type | Class and Description |
---|---|
class |
UnitValueVolume
A base class for a value that describes a volume measurement on the image.
|
class |
VolumePhysical
Volume expressed in cubic meters, or units thereof.
|
class |
VolumeVoxels
Volume expressed in voxels.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureEnergy<T extends FeatureInputEnergy>
A base class for features that only require an input that extends from
FeatureInputEnergy |
class |
FeatureHistogram
A base class for features that accept a histogram as input.
|
class |
FeatureImageMetadata
A base class for a feature that accepts a
FeatureInputImageMetadata as input. |
class |
FeatureStack |
class |
VoxelScore
Calculates a per-voxel score.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureEvaluator<T extends FeatureInput>
Defines a feature and provides a means to calculate inputs for it, a session.
|
class |
FeatureListEvaluator<T extends FeatureInput>
Defines a list of features and provides a means to calculate inputs for it, a session.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureHistogramStatistic
Base class for
FeatureHistogram implementations that calculate a statistic from the
Histogram . |
Modifier and Type | Class and Description |
---|---|
class |
FeatureObjectCollection
A base class for a feature that accepts a
ObjectCollection as input. |
Modifier and Type | Class and Description |
---|---|
class |
FeatureDeriveFromPair
Base class for evaluating
FeaturePairObjects in terms of another feature that operations
on elements (first, second, merged etc.) |
class |
FeaturePairObjects |
class |
First
Evaluates the first-object in a pair only
|
class |
Merged
Evaluates the first-object in a pair only
|
class |
RatioFirstToSecond
Ratio of first-object to second-object in a pair.
|
class |
Second
Evaluates the first-object in a pair only
|
class |
SubtractSecondFromFirst
Subtract second-object from first-object in a pair.
|
Modifier and Type | Class and Description |
---|---|
class |
CenterOfGravity |
class |
FeatureSingleObject |
class |
NumberVoxels |
Modifier and Type | Class and Description |
---|---|
class |
ConvertFromPhysicalVolume<T extends FeatureInputWithResolution>
converts a feature to a physical distance in a XY place that is isometric
|
class |
ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> |
class |
ConvertToPhysicalDistance<T extends FeatureInputWithResolution> |
class |
ConvertToPhysicalVolume<T extends FeatureInputWithResolution>
converts a feature to a physical distance in a XY place that is isometric
|
class |
FeatureConvertUnits<T extends FeatureInputWithResolution> |
class |
WithResolutionBase<T extends FeatureInputWithResolution>
Base-class for a feature that requires input-resolution to be calculated.
|
Modifier and Type | Class and Description |
---|---|
class |
ReduceElementsGreedy
Reduces the number or spatial-extent of elements by favouring higher-confidence elements over
lower-confidence elements.
|
class |
RemoveOverlappingObjects
Intersecting objects are removed if they have sufficient overlap.
|
Modifier and Type | Class and Description |
---|---|
class |
DecodeInstanceSegmentation<T>
Decodes inference output into segmented-objects.
|
class |
SegmentStackIntoObjectsPooled<T extends InferenceModel>
A base class for algorithms to segment a stack into one or more objects - using a pool of models
|
class |
SegmentStackIntoObjectsScaleDecode<T,S extends ImageInferenceModel<T>>
A
SegmentStackIntoObjectsScaleDecode that scales the input image, before performing
inference, and then decodes the output. |
class |
SuppressNonMaximum<T extends InferenceModel>
Applies a segmentation procedure followed by non-maximum suppression.
|
Modifier and Type | Class and Description |
---|---|
class |
ReduceElements<T>
Reduces the number or spatial-extent of elements by favoring higher-confidence elements over
lower-confidence elements.
|
Modifier and Type | Class and Description |
---|---|
class |
ChannelMapCreator
Creates a
ChannelMap for a particular OpenedImageFile . |
class |
IndexedChannel
A particular
Channel to be read from a file, identified by its position (index) in the
file. |
Modifier and Type | Class and Description |
---|---|
class |
Filled
Draws a filled-in shape for each object.
|
class |
Flatten
Performs a flattening (maximum intensity projection in each channel) of the output of another
writer
|
class |
IfElse
Branches to two different
DrawObject depending on a predicate. |
class |
Outline
Draws the outline of each object-mask.
|
Modifier and Type | Class and Description |
---|---|
class |
OutputFeatureTable
Specifies a table of feature-calculations on objects.
|
Modifier and Type | Class and Description |
---|---|
class |
StackProviderWithLabel
Combines a
Provider<Stack> with a label. |
class |
TextStyle
The size and style of text as it should appear in an image.
|
class |
TileWithLabels
Tiles a number of
StackProviderWithLabel s as a single StackProvider . |
class |
WriteText
Creates an image that contains text only.
|
Modifier and Type | Class and Description |
---|---|
class |
FromStackReader
Uses a
StackReader to read the image-metadata. |
class |
ImageMetadataReader
Reads an
ImageMetadata from the file-system. |
Modifier and Type | Class and Description |
---|---|
class |
InputManagerWithStackReader<T extends InputFromManager>
Extends an
InputManager to add a StackReader bean property. |
class |
StackReader
Reads an image-
Stack from the file-system. |
class |
StackReaderOrientationCorrection
A
StackReader that supports the correction of orientation as images are read from the
file-system. |
Modifier and Type | Class and Description |
---|---|
class |
OneOrThreeChannelsWriter
A base-class for a
StackWriter that writes an image that has either one or three
channels. |
class |
StackWriter
Writes a stack (i.e.
|
Modifier and Type | Class and Description |
---|---|
class |
BioformatsReader
Reads a stack using the Bioformats
library.
|
Modifier and Type | Class and Description |
---|---|
class |
Default |
class |
ForceBitsPerPixel |
class |
ForceChannelsPerByteArray |
class |
ForceNumberChannels |
class |
ForceNumberFrames |
class |
ForceTimeSeriesToStack
Treats a time-series as if it was a z-stack
|
class |
ReadOptions
Options that influence how stack is read in
BioformatsReader . |
class |
ReadOptionsDelegate
Forces a particular settings, but otherwise uses settings from a delegate
|
class |
SwitchChannelTime
Treats the channel index as if it's time, and vice versa
|
Modifier and Type | Class and Description |
---|---|
class |
BioformatsWriter
Base class for writing a stack to the filesystem using the Bioformats library.
|
class |
OMETiff
Writes a stack to the filesystem as an OME-TIFF using the Bioformats library.
|
class |
OMEXML
Writes a stack to the filesystem as an OME-XML using the Bioformats library.
|
class |
Tiff
Writes a stack to the filesystem as a TIFF using the Bioformats library.
|
Modifier and Type | Class and Description |
---|---|
class |
ImageJ
Resizes with linear
interpolation as implemented in ImageJ.
|
Modifier and Type | Class and Description |
---|---|
class |
ImageJRasterWriter
Base class for writing a raster using ImageJ.
|
Modifier and Type | Class and Description |
---|---|
class |
InputManager<T extends InputFromManager>
Base class for describing the inputs.
|
class |
InputManagerUnary<T extends InputFromManager>
Base class for an
InputManager that delegates to another InputManager with the
same input-type. |
Modifier and Type | Class and Description |
---|---|
class |
ReadFromFile
Reads a
Dictionary from a file in Java
properties format. |
Modifier and Type | Class and Description |
---|---|
class |
FilesProvider
Base class for providing a list of
File s. |
class |
FilesProviderUnary
Like
FilesProvider but employs a unary operator on a call to an existing FilesProvider . |
class |
FilesProviderWithDirectory
Base class for implementations of
FilesProvider which do have an associated
directory. |
class |
FilesProviderWithDirectoryString
A
FilesProviderWithDirectory where the directory is optionally specified as a string
constant |
class |
FilesProviderWithDirectoryUnary
Like
FilesProviderWithDirectory but employs a unary operator on a call to an existing
FilesProviderWithDirectory . |
class |
FilesProviderWithoutDirectory
Base class for implementations of
FilesProvider which do not have an associated
directory. |
class |
SearchDirectory
Searches a directory for files whose paths match a particular predicate.
|
class |
SingleFile
Provides a single file only.
|
class |
SpecificPathList
A specific list of paths which form the input.
|
Modifier and Type | Class and Description |
---|---|
class |
FromDerivePath
Derives the grouping-key via a call to
DerivePath . |
class |
Grouper
Determines how partition inputs into groups.
|
class |
WithoutGrouping
Avoids grouping of inputs, effectively processing all inputs as one large group.
|
Modifier and Type | Class and Description |
---|---|
class |
FileNamer
Associates a name (a compact unique identifier) with a file.
|
class |
FileNamerIndependent
Base class for methods that derive the name independently for each file.
|
Modifier and Type | Class and Description |
---|---|
class |
DerivePath
Derives a path from an existing path.
|
class |
Identity
Returns the same
Path as the argument passed in. |
class |
NameElementRange
|
Modifier and Type | Class and Description |
---|---|
class |
FilePathMatcher
Matches file-paths against some kind of pattern.
|
class |
MatchExtensions
Maybe imposes a file-extension condition, optionally on top of an existing matcher.
|
class |
MatchGlob
Matches paths using a Java-style glob.
|
class |
MatchRegularExpression
Predicates that matches a file-path against a regular expression.
|
Modifier and Type | Class and Description |
---|---|
class |
FilePathProvider
|
class |
FilePathProviderReference
Calls an existing
FilePathProvider indirectly to provide an identical result. |
class |
FromFiles
Extracts a path from a
FilesProvider . |
Modifier and Type | Class and Description |
---|---|
class |
OutputManager
Responsible for making decisions on where output goes and what form it takes.
|
class |
OutputWriteSettings
Settings for how to write output, including default writers.
|
class |
ReportFeature<T> |
Modifier and Type | Class and Description |
---|---|
class |
IgnoreUnderscorePrefix
All outputs are allowed unless the name's first character is an underscore.
|
class |
OutputEnabled
Whether a particular output, identified by a textual name, is enabled or not.
|
class |
SpecificDisabled
Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
|
class |
SpecificEnabled
Only specific outputs, identified by a textual name, are enabled.
|
Modifier and Type | Class and Description |
---|---|
class |
IncrementingNumber
Outputs an incrementing number for each output that occurs.
|
class |
PathPrefixer |
class |
PathPrefixerAvoidResolve
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
|
Modifier and Type | Class and Description |
---|---|
class |
AddToDefaults
Adds additional outputs-names to be enabled to the defaults.
|
class |
IgnoreUnderscorePrefixUnless
Like
IgnoreUnderscorePrefix for all first and level-outputs unless a particular outputs
are explicitly specified. |
class |
NoneExcept
All outputs are disabled except particular ones.
|
class |
OutputEnabledRules
Bean that specifies an implementation of
MultiLevelOutputEnabled . |
class |
OutputEnableRulesSpecify
Base class for an
OutputEnabledRules that specifies particular output-names for first and
second levels. |
class |
Permissive
Allows all output-names to be outputted in both first and second level.
|
class |
PermissiveExcept
All outputs are enabled except particular ones.
|
Modifier and Type | Class and Description |
---|---|
class |
HelloWorld<S extends InputFromManager>
A dummy task that simply writes a message to all log files, specifically: 1.
|
Modifier and Type | Class and Description |
---|---|
class |
AnnealScheme
Base class for approaches to simulated annealing.
|
class |
MarksBean<T> |
Modifier and Type | Class and Description |
---|---|
class |
Bound |
class |
BoundDegrees |
class |
BoundMinMax |
class |
BoundPhysicalExtent |
class |
BoundUnitless |
class |
MarkBounds |
class |
ResolvedBound
A bound resolved into pixel units
|
Modifier and Type | Class and Description |
---|---|
class |
BoundRotation |
class |
BoundRotation2D
Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
|
class |
BoundRotation3D
Creates a randomly-generated orientation in 3D based upon Euler Angles
|
Modifier and Type | Class and Description |
---|---|
class |
MarkRegion |
Modifier and Type | Class and Description |
---|---|
class |
MarkEllipseFactory |
class |
MarkEllipsoidFactory |
class |
MarkFactory |
class |
MarkPointListFactory |
class |
MarkWithIdentifierFactory |
Modifier and Type | Class and Description |
---|---|
class |
CreateMarkFromPoints |
class |
PointsBean<T> |
Modifier and Type | Class and Description |
---|---|
class |
PointsFitter |
Modifier and Type | Class and Description |
---|---|
class |
MarkCollectionProposer
Proposes an entire collection (confguration) of marks
|
class |
MarkFromCollectionProposer |
class |
MarkMergeProposer |
class |
MarkProposer |
class |
MarkSplitProposer |
class |
OrientationProposer |
class |
PointsProposer |
class |
PositionProposer |
class |
ProposerBean<T> |
class |
RadiiProposer |
class |
ScalarProposer |
Modifier and Type | Class and Description |
---|---|
class |
MarkBoundsProvider |
class |
MarkCollectionProvider
Provides a collection of marks
|
class |
MarksBaseProvider<T,S>
|
class |
SingleMarkProvider
Provides (maybe) a single mark
|
Modifier and Type | Class and Description |
---|---|
class |
RegionMap
Maps integer IDs to sub-regions in the map
|
class |
RegionMembership |
class |
RegionMembershipAnd |
class |
RegionMembershipOr |
Modifier and Type | Class and Description |
---|---|
class |
AddCriteriaOr |
class |
AddCriteriaPair |
class |
ArbitraryPointCommon
If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
|
class |
BoundingBoxIntersection |
class |
RandomCollectionWithAddCriteria<T>
An implementation of a
RandomCollection that uses AddCriteria |
Modifier and Type | Class and Description |
---|---|
class |
AsSingle
Extracts one of the memos from the pair, and processes as a
FeatureSingleMemo |
class |
FeatureAllMemo |
class |
FeaturePairMemo |
class |
FeatureSingleMemo |
Modifier and Type | Class and Description |
---|---|
class |
EnergySchemeCreator |
class |
EnergySchemeCreatorByElement |
Modifier and Type | Class and Description |
---|---|
class |
CheckMark
A predicate on a mark to check if a condition has been satisfied.
|
class |
FeatureMark |
class |
MarkEvaluator |
class |
PxlListOperationFromMark |
Modifier and Type | Class and Description |
---|---|
class |
FeatureMarkCollection |
Modifier and Type | Class and Description |
---|---|
class |
MarkPairCollection
A pair collection where the underlying type is a simple
MarkPair |
Modifier and Type | Class and Description |
---|---|
class |
MultiInputManager |
Modifier and Type | Class and Description |
---|---|
class |
ReportFeatureEvaluator<T extends FeatureInput> |
class |
ReportFeatureForMarks<T extends FeatureInput> |
class |
ReportFeatureForSharedObjects |
class |
ReportFeatureOnMark |
class |
ReportFeatureOnMarks |
class |
ReportFeatureOnObject |
class |
ReportFeatureOnObjectCollection |
class |
ReportFeatureOnObjectsBase<T extends FeatureInput> |
class |
ReportFeatureWrapError |
Modifier and Type | Class and Description |
---|---|
class |
RandomCollection<T>
A collection of items from which one can randomly sample
|
Modifier and Type | Class and Description |
---|---|
class |
SegmentIntoMarks |
Modifier and Type | Class and Description |
---|---|
class |
DefineOutputter
After using applying a
Define on inputs, output produced entities (images, histograms,
objects etc.) |
Modifier and Type | Class and Description |
---|---|
class |
OptimizationScheme<S,U,V>
An optimization-scheme that uses kernels to make changes to state.
|
Modifier and Type | Class and Description |
---|---|
class |
ExtractScoreSize<T> |
class |
FeedbackReceiverBean<T> |
class |
FeedbackReceiverList<T> |
class |
FeedbackReceiverRequireArguments<T> |
class |
PeriodicSubdirectoryReporter<T> |
class |
ReporterAggregate<T> |
class |
ReporterInterval<T> |
class |
StateReporter<T,S>
Converts the optimization state to a form that the reporter needs
|
Modifier and Type | Class and Description |
---|---|
class |
Kernel<T,S>
Modifies an entity by applying a kernel.
|
class |
KernelIndependent<T,S>
A kernel that makes proposals independently of the current state.
|
class |
KernelPosNeg<T,S> |
class |
KernelProposer<T,S> |
class |
KernelProposerOption<T,S> |
Modifier and Type | Class and Description |
---|---|
class |
TerminationCondition
A condition on whether to terminate the optimization or continue with further steps.
|
class |
TerminationConditionListOr
Conditions that are combined together in a logical OR to form a single
termination-condition.
|
class |
TriggerTerminationCondition |
Modifier and Type | Class and Description |
---|---|
class |
Compose<S,T,U>
Combines a transformation from
S to U with one from U to T |
class |
StateTransformerBean<S,T>
Transforms one type into another.
|
Modifier and Type | Class and Description |
---|---|
class |
DrawObject
Draws a representation of an
ObjectMask on a RGBStack . |
Modifier and Type | Class and Description |
---|---|
class |
AggregateAnnotations<S extends AnnotatorStrategy>
Aggregates many per-image annotations together in form of a CSV file.
|
Modifier and Type | Class and Description |
---|---|
class |
DualMarksAnnotationAsObjects<T>
|
class |
MarksAsObjects
|
class |
MaskAsObject
Loads
Mask to compared, converting it into an ObjectMask . |
class |
Objects
An
ObjectCollection to be compared against something else. |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationComparisonInputManager<T extends InputFromManager> |
class |
CompareAnnotations<T extends Assignment<ObjectMask>>
Task to compare a set of annotations to a segmentation or another set of annotations.
|
Modifier and Type | Class and Description |
---|---|
class |
AnnotationComparisonAssigner<T extends Assignment<ObjectMask>>
Compares elements in an annotation to elements from an experiment.
|
class |
FeatureCostAssigner
Assigns an objects from one set of objects to another based upon a cost (degree of overlap).
|
class |
MaskIntersectionAssigner
No outputs are produced.
|
Modifier and Type | Class and Description |
---|---|
class |
FromAnnotations<T extends AnnotatorStrategy> |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationLabel |
Modifier and Type | Class and Description |
---|---|
class |
ImageLabelStrategy
Assigns a single label per image, as a whole.
|
class |
MarkProposerStrategy
Annotates each image with a mark
|
class |
SinglePathStrategy
A base class for implementations of
AnnotatorStrategy where a single unique path exists
for every annotation. |
Modifier and Type | Class and Description |
---|---|
class |
GrayscaleReconstruction2DIJ |
Modifier and Type | Class and Description |
---|---|
class |
AnisotropicDiffusion
Performs Perona-Malik Anisotropic
Diffusion.
|
class |
MinimumFilter |
Modifier and Type | Class and Description |
---|---|
class |
DistanceTransform3D
Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
|
class |
DistanceTransformForEachObject3D
Like
DistanceTransform3D but applies the distance transform separately for each object in
a collection. |
Modifier and Type | Class and Description |
---|---|
class |
AddDistanceTransform
Performs a Watershed on
distance transform by bundling
together several other beans.
|
Modifier and Type | Class and Description |
---|---|
class |
AutoLocalThreshold
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
|
Modifier and Type | Class and Description |
---|---|
class |
ThresholderAutoIJ |
Modifier and Type | Class and Description |
---|---|
class |
BlurGaussian3D
Performs a Gaussian Blur in 3D
|
class |
BlurGaussianEachSlice2D
Performs a Gaussian-blur in 2D on each slice independently
|
class |
BlurStrategy
A method for applying blurring to an image
|
Modifier and Type | Class and Description |
---|---|
class |
MaxProjection<T>
Maximum-intensity-projection
across
Channel s. |
class |
MeanProjection<T>
Mean-intensity-projection across
Channel s. |
class |
MinProjection<T>
Minimum-intensity-projection across
Channel s. |
class |
ProjectableBufferAggregator<T>
An aggregator that calculates the aggregation of every voxel across successive channels
via a
ProjectableBuffer . |
class |
StandardDeviationProjection<T>
Projection of the standard-deviation of voxels values across all inputs.
|
Modifier and Type | Class and Description |
---|---|
class |
ScaleByDictionary
Scales by compressing a certain range of values into the 8-bit signal.
|
class |
ScaleByMinMaxValue
Scales by compressing a certain range of values into the 8-bit signal
|
class |
ScaleByTypeToByte |
class |
ToByte |
class |
ToByteUpperLowerQuantileIntensity |
Modifier and Type | Class and Description |
---|---|
class |
CreateNew
Creates a new channel with all values initialized to a constant (by default zero)
|
class |
Duplicate |
class |
FromInput
Finds the input-stack using a conventional name of
input_image - and extracts the first
channel |
class |
FromStack
Extracts a channel from a provider of a stack
|
class |
IfParamEquals |
class |
TwoVoxelMappingBase
Takes the two channels and creates a NEW third channel whose pixels are a function of the two
channels
|
class |
UnaryWithObjectsBase |
class |
UnaryWithValueBase
A
ChannelProviderUnary which has a scalar value field |
Modifier and Type | Class and Description |
---|---|
class |
AddConstant |
class |
ArithmeticWithConstantBase
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
|
class |
ArithmeticWithConstantConditionallyWriteBase |
class |
Invert
Subtracts each voxel from the maximum value for the channel's data type (e.g.
|
class |
MaxTwoChannels |
class |
MaxWithConstant |
class |
MeanThreeChannels
Creates a new channel that is the mean of three input channels
|
class |
MinTwoChannels |
class |
MinWithConstant |
class |
MultiplyConstant |
class |
MultiplyTwoChannels |
class |
SubtractFromConstant |
class |
SubtractMean
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
|
class |
SubtractTwoChannels |
Modifier and Type | Class and Description |
---|---|
class |
AssignFromChannel
Copies the pixels from
channelAssignFrom to channel (possibly masking) |
class |
AssignFromDictionary |
class |
AssignFromIntersectingObjects
Matches source-objects to target objects, based upon intersection, and assigns the value in the
respective source object to the target object
|
class |
AssignValue
Assigns a constant (scalar) value to the portion of the image covered by a mask
|
Modifier and Type | Class and Description |
---|---|
class |
Convert<T>
Converts a channel by applying a converter (no histogram is involved in the conversion).
|
class |
ConvertBase |
class |
ConvertWithHistogram<T>
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
|
Modifier and Type | Class and Description |
---|---|
class |
GradientBase
Base class to calculate the gradient of the voxels in a
Channel . |
class |
GradientBaseAddSum
Like
GradientBase but allows an arbitrary constant to be added to voxels storing the
gradient. |
class |
GradientForAxis
Extracts the gradient in the direction of a particular axis (identified by an index)
|
class |
GradientXY
Calculates a
Channel 's gradient along the x and y axes. |
class |
Sobel
3x3 Sobel Filter
|
Modifier and Type | Class and Description |
---|---|
class |
Blur
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
|
class |
IfVoxelZero
Creates a new channel which is a merged version of two input channels according to rules.
|
class |
NormalizeDifferenceToMedian
Corrects a channel in the following way
|
class |
NormalizeObjectIntensity
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
|
class |
QuantileStretch
Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel
data range
|
class |
ScaleXY
Scales the channel in the X and Y dimensions.
|
Modifier and Type | Class and Description |
---|---|
class |
FromMask |
class |
FromMaskBase
A base class for a
ChannelProvider which also uses a binary-mask, but which doesn't use
any other ChannelProvider as an input. |
class |
UnaryWithMaskBase |
class |
ZeroOutsideMask
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelPerObjectBase
Creates a channel with a level calculated for each object variously
|
class |
LevelPerObjectIndependently
Creates a channel with different threshold-levels for each object, calculating the level only
from the histogram of the particular object.
|
class |
LevelPerObjectNeighbors
Calculates a threshold-level for each object collectively based on other objects
|
Modifier and Type | Class and Description |
---|---|
class |
IdentifyObjects
Assigns a unique id number to each object.
|
class |
ScoreObjects |
class |
ScoreVoxels
Assigns a score (a value indicating how probable something is) to each voxel
|
Modifier and Type | Class and Description |
---|---|
class |
ExtractCenterSlice
Extracts the slice at the center (rounding down) of the range of z-stacks.
|
class |
ExtractSliceRange
Extracts slices from
sliceStart (inclusive) to sliceEnd (inclusive). |
class |
MaximumIntensityProjection |
class |
MeanIntensityProjection |
class |
RepeatSlice
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
|
Modifier and Type | Class and Description |
---|---|
class |
GenerateToMatchObjects
Generates colors to match the size of an object-collection.
|
Modifier and Type | Class and Description |
---|---|
class |
DictionaryCondition
Checks if a value in a
Dictionary is equal to an expected-value. |
Modifier and Type | Class and Description |
---|---|
class |
GuessDimensions
Guesses dimensions from an input-image if it exists.
|
class |
SpecifyDimensions
Specifies dimensions explicitly via bean properties.
|
Modifier and Type | Class and Description |
---|---|
class |
CutBelowThreshold
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
|
class |
GreaterThanThreshold
Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the
threshold
|
Modifier and Type | Class and Description |
---|---|
class |
CalculateLevelListBase |
class |
CalculateLevelRelativeToThreshold |
class |
ClampHistogramMax
Clamps the input-histogram to a certain maximum value, and then delegates the calculate-level.
|
class |
EmptyHistogramConstant
Specifies a constant if a histogram is empty, otherwise delegates to another {#link
org.anchoranalysis.image.bean.threshold.CalculateLevel}
|
class |
IfGreaterThan
Calculates a level from the first delegate and if greater than a threshold, recalculates from a
second delegate.
|
class |
IfLessThan
Calculates a level from the first delegate and if less than a threshold, recalculates from a
second delegate.
|
class |
Otsu
Performs auto-thresholding using Otsu's method.
|
class |
OtsuWeighted
Similar to Otsu, but weighs the variances differently of background and foreground.
|
Modifier and Type | Class and Description |
---|---|
class |
AllValuesOff
Creates a new mask of particular dimensionality where all values are off.
|
class |
AllValuesOn
Creates a new mask of particular dimensionality where all values are on.
|
class |
FromChannelBase
Base-class for
MaskProvider s that accept a Channel as input. |
Modifier and Type | Class and Description |
---|---|
class |
And
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the
result.
|
class |
CombineBase |
class |
IfHighLow
Outputs the logical operation
iff first==HIGH and second==LOW then LOW voxelwise on both
masks, modifying {mask} with the result. |
class |
Or
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the
result.
|
class |
Xor
Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask}
with the result.
|
Modifier and Type | Class and Description |
---|---|
class |
FromChannel
Creates a mask from an existing channel, reusing the channel's buffer and considering all 0
values as off, and 255 values as on.
|
class |
FromStackChannel |
Modifier and Type | Class and Description |
---|---|
class |
Box
Creates a
Mask where all pixels are on within a box region. |
class |
Dilate
Performs a dilation morphological operation on
BinaryVoxels . |
class |
ExteriorContour
Finds the exterior outer contour for a
Mask that forms its outline. |
class |
FitBoxToOnVoxels
Fits a box around the on voxels.
|
class |
MorphologicalOperatorBase
Base class for performing morphological operations on
BinaryVoxels . |
Modifier and Type | Class and Description |
---|---|
class |
IfKeyValueCondition
The current
mask is returned if a condition on key-values is satisfied otherwise maskElse is returned. |
class |
IfNotEmpty
The current
mask is returned if it's non-empty (at least one on voxel) otherwise
maskElse is returned. |
class |
IfObjectFilter
The current
mask is returned if the mask (treated as an object) passed an object-filter,
otherwise maskElse is returned. |
class |
IfPredicateBase
Base class which multiplexes between the current mask and an alternative depending if a condition
is met.
|
class |
IfStackExists
The current
mask is a particular stack exists (at least one on voxel) otherwise
maskElse is returned. |
Modifier and Type | Class and Description |
---|---|
class |
SegmentChannel
Applies a
BinarySegmentation algorithm to derive a mask from a channel |
class |
Threshold
Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel
if possible.
|
Modifier and Type | Class and Description |
---|---|
class |
FlattenZ
Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity
projection).
|
Modifier and Type | Class and Description |
---|---|
class |
ObjectFilterPredicate
Uses a predicate to make a decision whether to keep objects or not.
|
class |
ObjectFilterRelation
An independent object-filter that uses a relation in its predicate.
|
Modifier and Type | Class and Description |
---|---|
class |
DiscardOutliers
Calculates features values for all objects, and discards any object less than
quantile - (minRatio * stdDev) |
class |
RelationWithMatches
Matches each object with others, and keeps only those where a relation holds true for all matches
(in terms of features)
|
Modifier and Type | Class and Description |
---|---|
class |
ObjectFilterCombine
A filter that combines other filters (in a list)
|
Modifier and Type | Class and Description |
---|---|
class |
GreaterIntersectionWith
Only accepts an object if it has greater (or EQUAL) intersection with
objectsGreater than
objectsLesser |
class |
IntensityGreaterEqualThan
Only keep objects where at least one voxel (on a particular channel) has intensity greater or
equal to a threshold.
|
class |
IntersectsWith
Keeps objects which intersects with ANY ONE of a collection of other objects.
|
class |
NotTouchingSceneBorder
Keeps only objects that are not adjacent to the scene-border (i.e.
|
class |
ThresholdedFeature
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
|
class |
ThresholdedVolume
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
|
Modifier and Type | Class and Description |
---|---|
class |
Always
Specifies a single object that will always be the "match" for whatever source object.
|
class |
Bridge
Matches to another object, and then uses that object to bridge to another
|
Modifier and Type | Class and Description |
---|---|
class |
AtIndex
Extract a single
ObjectMask into a new collection. |
class |
Empty
Creates an empty object-collection.
|
class |
IfParamEqual
Multiplexes between two object-collection-providers depending on whether a parameter value equals
a particular string
|
class |
Permute
Permutes some changes over an
ObjectCollectionProvider and collects all the results in an
ObjectCollection |
class |
ReferenceOrElse
Returns a object-collection by name if it exists, or else calls
objectsElse if it doesn't
exist. |
class |
Scale
Scales all the objects in the collection by a particular scale-factor.
|
class |
UnaryWithChannelBase |
class |
WithChannelBase |
class |
WithContainerBase
Base class for
ObjectCollectionProvider that take an optional objectsContainer
bean-field. |
class |
WithDimensionsBase
Base class for
ObjectCollectionProviderUnary classes that require dimensions to be
specified. |
class |
WithOptionalDimensionsBase
Base class for
ObjectCollectionProviderUnary classes that offer an optional means to
specify dimensions. |
Modifier and Type | Class and Description |
---|---|
class |
ConnectedComponentsFromMask
Converts a binary-mask into its connected components
|
class |
DecomposeIntoConnectedComponents
Ensures each object in a collection is a connected-component, decomposing it if necessary into
multiple objects.
|
class |
RejectIfNotConnected
Rejects a set of objects, if any object is not fully connected (pixels form two or more separate
connected components)
|
Modifier and Type | Class and Description |
---|---|
class |
ObjectCollectionProviderWithFeature |
class |
ObjectWithMaximumFeature
Finds the object with the maximum feature-value from a collection.
|
class |
ObjectWithMaximumFeatureFromEachMatchedCollection
Finds the object with the maximum feature among a group of matches for each object.
|
class |
SortByFeature
Creates a new object-collection with objects sorted by a derived feature-value (in ascending
order)
|
Modifier and Type | Class and Description |
---|---|
class |
Filter |
class |
FilterByGroup |
class |
IntersectsWithContainer
Returns only the objects that intersect with at least one object in the container
|
class |
Match |
class |
NotInContainer
Filters objects to keep only those which are NOT in the container.
|
class |
ObjectCollectionProviderFilterBase |
class |
RemoveTouchingBorder
Considers all possible pairs of objects in a provider, and removes those that touch the border.
|
Modifier and Type | Class and Description |
---|---|
class |
AndObjectsWithMasks
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
|
Modifier and Type | Class and Description |
---|---|
class |
MergeBase
A base class for algorithms that merge object-masks.
|
class |
MergeGreedyToIncreaseObjectFeature
Naive greedy merge strategy when any two neighboring objects are merged if it increases a
feature.
|
class |
MergePairs
Merges objects if a pair feature value satisfies a condition.
|
class |
MergeToIncreaseObjectFeature
Merges neighboring objects if it results in an increase in the average feature-value calculated
on each single object.
|
class |
MergeTwoCollectionsItemwise
Merges itemwise objects from two collections.
|
class |
MergeWithFeature
Base class for object-merging strategies that involve calculating a feature.
|
class |
MergeWithOptionalDistanceConstraint
Expands
MergeBase by optionally imposing a maximum-distance requirement between objects
that are possibly merged. |
Modifier and Type | Class and Description |
---|---|
class |
ObjectCollectionProviderMorphological |
Modifier and Type | Class and Description |
---|---|
class |
BinarySegmentByObject
Performs a binary-segmentation using the upstream objects as masks.
|
class |
SegmentChannelByObject
Performs segmentation of a channel using each object in the upstream collection as a mask.
|
class |
SegmentStack<T extends InferenceModel>
Segments a stack into objects.
|
class |
SegmentWithSeeds
Takes each object one-by-one from
objectsSource , and finds matching seeds from objectsSeeds |
Modifier and Type | Class and Description |
---|---|
class |
ExtendInZ
Creates a 3D version of an object by replicating each input-object across the z-dimension to meet
(3D) dimensions.
|
class |
ExtendInZWithinContainer
Extends an object (2D/3D) as much as it can within the z-slices of a containing object
|
class |
SliceAt |
Modifier and Type | Class and Description |
---|---|
class |
RemoveIntersectingVoxels
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
|
class |
SplitByObjects |
class |
SplitIntoSquares
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
|
Modifier and Type | Class and Description |
---|---|
class |
AtScale
Perform a segmentation at a different scale, and then fit the results back to the original scale.
|
class |
ConnectedComponentsFromBinarySegmentation
Performs a binary-segmentation of the channel and converts its connected-components into objects
|
class |
ImposeMinima
Imposes minima in seed locations on the input-channel before performing the segmentation
|
class |
Mser
Applies the MSER algorithm from imglib2
|
class |
SegmentOnMaximumIntensityAndExpandInZ
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D
segmentation.
|
Modifier and Type | Class and Description |
---|---|
class |
MinimaImposition |
class |
MinimaImpositionGrayscaleReconstruction |
Modifier and Type | Class and Description |
---|---|
class |
GrayscaleReconstructionByErosion |
class |
GrayscaleReconstructionRobinson |
Modifier and Type | Class and Description |
---|---|
class |
WatershedYeong
A 'rainfall' watershed algorithm
|
Modifier and Type | Class and Description |
---|---|
class |
ThresholdConfidence
Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
|
Modifier and Type | Class and Description |
---|---|
class |
ConstantScaleFactor
Scale X and Y dimension by a constant floating-point number.
|
class |
FitTo
Scales an image to approximately similar in size to a
SizeXY . |
class |
MinimumXYResolution |
class |
ToDimensions
Calculates a scaling-factor to make the source image have identical dimensions as
dimensionsTarget . |
class |
ToSuggested
Scales to the suggested-size if one is provided, otherwise calls
fallback . |
Modifier and Type | Class and Description |
---|---|
class |
Sequence
Performs a sequence of succesive segmentations
|
class |
ThresholdAgainstChannel
Thresholds each voxels by comparing against another channel that has per-voxel thresholds
|
Modifier and Type | Class and Description |
---|---|
class |
FromChannelOrMask
Creates a stack from a channel or mask (reusing the voxel buffers)
|
Modifier and Type | Class and Description |
---|---|
class |
ColoredBase
Base class for providers that draw entities (an outline or filled) on a background
|
class |
ColoredBaseWithGenerator
Like
ColoredBase but uses a generator to determine the colors for the objects |
class |
ColoredMask
Draws a colored representation (outline or filled) of a
ObjectMask on a background |
class |
ColoredObjects
Draws a colored representation (outline or filled) of an
ObjectCollection on a background |
class |
ThreeChannels |
class |
ThreeColoredObjects
Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
|
Modifier and Type | Class and Description |
---|---|
class |
OutlinePreserveRelativeSize
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.
|
class |
ThumbnailFromObjects
Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects
|
Modifier and Type | Class and Description |
---|---|
class |
ScaleToSize
Create a thumbnail by scales an image to a particular size.
|
class |
ThumbnailFromStack
Creates a thumbnail from a stack
|
Modifier and Type | Class and Description |
---|---|
class |
Area<T extends FeatureInputEnergy>
Area of the stack (XY dimensions only, Z dimension is not considered).
|
class |
Extent<T extends FeatureInputEnergy>
Width/height/depth of energy-stack in pixels depending on axis.
|
class |
ForSpecificAxis<T extends FeatureInputEnergy>
Dimensions-calculation for one specific axis only.
|
class |
FromDimensionsBase<T extends FeatureInputDimensions>
Base class for features that are calculated from
Dimensions . |
class |
VoxelPhysicalSize<T extends FeatureInputEnergy>
The physical size of a pixel in a specific dimension.
|
Modifier and Type | Class and Description |
---|---|
class |
CoefficientOfVariation
Calculates the coefficient of
variation of all the values in the histogram.
|
class |
Count
Counts the number of items in a histogram (posssibly in relation to a threshold: above, below
etc.)
|
class |
Kurtosis
Calculates the kurtosis of all the values in
the histogram.
|
class |
MeanRaisedToPower
Calculates the mean value in a histogram, and raises it to a power.
|
class |
Median |
class |
Mode
Calculates the skewness of all the
values in the histogram.
|
class |
NumberDistinctValues
Number of unique values in histogram.
|
class |
Quantile |
class |
RatioNonMode |
class |
Skewness
Calculates the skewness of all the values in
the histogram.
|
class |
StandardDeviation |
class |
TotalCount |
class |
Variance
Calculates the variance of all the values in
the histogram.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelFromHistogram
Calculates a level (a threshold-value) from a histogram.
|
class |
RatioThreshold |
class |
ThresholdHistogram
Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded
version.
|
Modifier and Type | Class and Description |
---|---|
class |
IntensityMoments
Calculate various moment-related statistics about the intensity of each channel of an image.
|
Modifier and Type | Class and Description |
---|---|
class |
DeriveFromPair
Embeds each feature in a
FeatureDeriveFromPair feature (first, second or
merge) and prepends with a string. |
class |
FeatureListProviderAggregatePair
Calculates features on each part of a pair (first, second, merged etc.) and then reduces the
calculation to a single number.
|
class |
ReduceFirstAndSecond
Calculates the aggregate of a feature applied to both the first and second objects in a
FeatureInputPairObjects . |
class |
ReduceRatioFirstAndSecond
Calculates the aggregate of the ratio of
first :second and second
:first for a FeatureInputPairObjects |
class |
SubtractReducedFromMerged
Calculates
merged - reduce(first,second) for a FeatureInputPairObjects |
Modifier and Type | Class and Description |
---|---|
class |
PermuteDivideByParam<T extends FeatureInputDictionary>
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
|
class |
PermuteFeature<S,T extends FeatureInput>
Permutes one or more properties of a Feature, so as to create a set of Features
|
class |
PermuteFeatureBase<T extends FeatureInput>
Creates permutations of a feature by modifying a particular property of it in different ways.
|
class |
PermuteFeatureSequenceInteger<T extends FeatureInputDictionary>
Permutes a property on a feature with a sequence of integers.
|
class |
PermuteFirstSecondOrder<T extends FeatureInputDictionary> |
class |
PermuteGaussianScore<T extends FeatureInputDictionary>
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
|
class |
PermuteZScore<T extends FeatureInputDictionary>
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
|
Modifier and Type | Class and Description |
---|---|
class |
BitDepthPerChannel
The bit-depth of the image per channel.
|
class |
NumberChannels
The number of channels in an image.
|
class |
NumberFrames
The number of frames in an image.
|
class |
NumberResolutionLevels
The number of resolution-levels in an image in a file.
|
class |
NumberSeries
The number of series in an image-file.
|
Modifier and Type | Class and Description |
---|---|
class |
MorphologicalIterations
Specifies a certain number of iterations of the morphological operations of dilation and erosion
|
Modifier and Type | Class and Description |
---|---|
class |
NumberObjects |
Modifier and Type | Class and Description |
---|---|
class |
CombineObjectsForFeatures<T extends FeatureInput>
A way to combine (or not combine) objects so that they provide a feature-table.
|
class |
EachObjectIndependently
Simply selects features directly from the list, and objects directly from the list passed.
|
class |
PairNeighbors
Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of
single-object features and pair features.
|
Modifier and Type | Class and Description |
---|---|
class |
Intersection
Finds the intersection of two objects and calculates a feature on it
|
Modifier and Type | Class and Description |
---|---|
class |
CostOverlapWithinMidpointDistance
TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
|
class |
OverlapRelative
Expresses the number of intersecting pixels between two objects as a ratio to something else
(denominator)
|
class |
OverlapRelativeToFirst |
class |
OverlapRelativeToMaxVolume
Overlap ratio to the maximum number of pixels
|
class |
OverlapRelativeToMerged |
class |
OverlapRelativeToSecond |
Modifier and Type | Class and Description |
---|---|
class |
HasTouchingVoxels
A simple scheme for counting the touching voxels.
|
class |
NumberTouchingVoxelFaces
A scheme for counting the touching voxels by intersection of object-masks
|
class |
NumberTouchingVoxels
A scheme for counting touching voxels.
|
class |
TouchingVoxels
Base class for features that calculate touching with a dilated bounding box intersection
|
Modifier and Type | Class and Description |
---|---|
class |
ArbitraryInsidePoint
Calculates deterministicly a point that is definitely inside the object-mask.
|
class |
OutlineKernelBase |
Modifier and Type | Class and Description |
---|---|
class |
AtBorderBase |
class |
AtBorderXY |
class |
AtBorderZ |
class |
NumberVoxelsAtBorder |
Modifier and Type | Class and Description |
---|---|
class |
BoundingBoxAlongAxisBase |
class |
BoundingBoxExtentAlongAxis |
class |
BoundingBoxMaximumAlongAxis |
class |
BoundingBoxMinimumAlongAxis |
class |
BoundingBoxNumberVoxels |
Modifier and Type | Class and Description |
---|---|
class |
CountEqual |
class |
NumberNeighboringVoxels
Calculates the number of voxels on the object that have a neighbor.
|
class |
SpecificEnergyChannelBase |
Modifier and Type | Class and Description |
---|---|
class |
FeatureEnergyChannel
A feature that uses a channel from the energy-stack as identified by an index
|
class |
IntensityMeanMaxSlice |
class |
IntensityMeanShell
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
|
class |
IntensityMeanShellBase
Constructs a shell around an object-mask using a standard dilation and erosion process
|
class |
IntensityMeanShellMaxSlice
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
|
class |
TextureScore
From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and
Classification of Heterogeneous Populations of Cell Nuclei
|
Modifier and Type | Class and Description |
---|---|
class |
GradientMagnitude
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
|
class |
GradientMeanForAxis
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular
direction
|
class |
IntensityGradientBase |
Modifier and Type | Class and Description |
---|---|
class |
ImageMomentsBase
A base class for features that are calculated using image-moments.
|
class |
PrincipalAxisEccentricity
Calculates the eccentricity of the Principal Axes (as defined by Image Moments).
|
class |
PrincipalAxisLength
The length of a principal-axis (as defined by Image Moments).
|
class |
PrincipalAxisOrientation
An element from orientation of a principal-axis (as defined by Image Moments).
|
class |
RatioPrincipalAxisLength
Calculates the ratio of prinicpal-axis length using Image Moments.
|
class |
SpecificAxisBase
A feature based one one-specific principal-axis as identified by image moments.
|
Modifier and Type | Class and Description |
---|---|
class |
DerivedObject |
class |
Erode |
class |
NumberRemovedVoxelsAfterClosing
How many pixels are removed after a morphological closing operation on the object-mask.
|
class |
Shell |
Modifier and Type | Class and Description |
---|---|
class |
ObjectRadiusStandardDeviation |
class |
ShapeRegularityCenterSlice |
class |
ShapeRegularityMIP |
Modifier and Type | Class and Description |
---|---|
class |
PairedWithMask
Evaluates the object as a pair-feature together with the binary-mask from the shared objects.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureIntersectingObjects |
class |
FeatureIntersectingObjectsSingleElement |
class |
FeatureIntersectingObjectsThreshold |
class |
MaxFeatureIntersectingObjects
1.
|
class |
MinFeatureIntersectingObjectsAboveThreshold
1.
|
class |
NumberIntersectingObjects |
class |
NumberIntersectingObjectsAboveThreshold
1.
|
Modifier and Type | Class and Description |
---|---|
class |
MaximumNumberContourVoxelsOnSlice
Maximum number of voxels on any slice's contour (edge voxels) across all slices.
|
class |
MaximumNumberVoxelsOnSlice
Maximum number of voxels in the object-mask across all slices.
|
Modifier and Type | Class and Description |
---|---|
class |
SurfaceNumberVoxelFaces
The number of voxel-faces along the surface (the faces of each voxel that touch outside)
|
class |
SurfaceNumberVoxels
The number of voxels on the surface (all voxels on the exterior of the object)
|
class |
SurfaceNumberVoxelsBase |
Modifier and Type | Class and Description |
---|---|
class |
UnitsWithinRange<T extends FeatureInputWithResolution>
Checks if a value lies within a range defined by units (a minimum and maximum boundary)
|
Modifier and Type | Class and Description |
---|---|
class |
CalculateLevel |
class |
CalculateLevelBase |
class |
Difference |
class |
DifferenceCalculateLevelStandardDeviation
Similar to
Difference but calculates the width as the standard-deviation of the histogram |
class |
FromDictionaryBase |
class |
IdentityImposeValueRelationToHistogram |
class |
NormalizeByConstant |
class |
NormalizeByMax
This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
|
class |
OutsideRange |
class |
RejectIfIntensityLessThan |
Modifier and Type | Class and Description |
---|---|
class |
ParamFromCollection<T extends FeatureInput>
Retrieves a parameter as stored in a
Dictionary in SharedObjects . |
Modifier and Type | Class and Description |
---|---|
class |
FeatureSingleObjectFromShared<T extends FeatureInputEnergy>
Calculates as object-masks from entities in shared, using the feature-input only for a
energy-stack.
|
class |
MaskAsSingleObject<T extends FeatureInputEnergy>
Calculate a feature, treating a mask as a single-object on the energy-stack
|
class |
MeanAcrossObjects<T extends FeatureInputEnergy>
Calculates the mean of a feature applied to each connected component
|
class |
ObjectAggregationBase<T extends FeatureInputEnergy>
Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
|
class |
QuantileAcrossObjects<T extends FeatureInputEnergy>
Calculates the quantile of a feature applied to each connected component
|
Modifier and Type | Class and Description |
---|---|
class |
DataTypeMaxIntensity<T extends FeatureInputEnergy>
The maximum-intensity allowed by the data-type of the stack.
|
Modifier and Type | Class and Description |
---|---|
class |
AsObjectMask
Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask
feature
|
class |
QuantileAcrossConnectedComponents
Calculates the median of a feature applied to each connected component
|
Modifier and Type | Class and Description |
---|---|
class |
RasterTask<S,U>
An experiment that takes (primarily) a series of raster images as an input.
|
Modifier and Type | Class and Description |
---|---|
class |
AggregateChannelTask
Creates a an aggregated-image for each group, where each voxel-value is aggregated across each
channel in each image in the group.
|
class |
Montage
Creates a montage of images, by tiling them side-by-side.
|
Modifier and Type | Class and Description |
---|---|
class |
ExportFeatures<T extends InputFromManager,S,U extends FeatureInput>
Calculates features and exports them as a CSV file.
|
class |
ExportFeaturesStyle
Visual style for how features are exported.
|
Modifier and Type | Class and Description |
---|---|
class |
FeatureSource<T extends InputFromManager,S,U extends FeatureInput>
Extracts features from some kind of inputs to produce one or more rows in a feature-table.
|
class |
FromHistogram
Each input-file describes a histogram that produces one row of features.
|
class |
FromImage
Calculates features from a single image.
|
class |
FromImageMetadata
Calculates features from the metadata from single image.
|
class |
SingleRowPerInput<T extends InputFromManager,S extends FeatureInput>
Base class for exporting features, where features are calculated per-image using a
NamedFeatureStore . |
Modifier and Type | Class and Description |
---|---|
class |
ConvertImageFormat
Converts each input-image to an output format, optionally changing the bit depth.
|
Modifier and Type | Class and Description |
---|---|
class |
ChannelConvertStyle
Converts a channel(s) at a particular timepoint into a stack(s).
|
class |
ExtractToRGB
Extracts three channels to make an RGB image.
|
class |
IndependentChannels
Converts each channel independently and creates a single-channeled stack from the conversion.
|
class |
RGBIfNamesMatch
Converts a set of channels to a single RGB-stack if the channel-names match, otherwise uses
fallback . |
Modifier and Type | Class and Description |
---|---|
class |
GroupedStackBase<S,T>
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
|
Modifier and Type | Class and Description |
---|---|
class |
ExportImageHistograms
Exports a histogram of voxel intensities as a CSV file for each channel of an image.
|
Modifier and Type | Class and Description |
---|---|
class |
All
Selects all possible channels from all possible stacks
|
class |
FromStacks
Selects a a subset of channels from a set of stacks
|
class |
One
Selects one specific channel from a set of stacks
|
class |
SpecificAndRename
Selects a specific set of channels from stacks, each identified by a stack-name and channel index
|
Modifier and Type | Class and Description |
---|---|
class |
BinaryClassifierImageLabeller |
class |
BinaryOutcomeImageLabeller |
class |
DescriptiveNameContainsImageLabeller |
class |
ImageAssignLabel<T>
Assigns a label to each image and copies into subdirectories for each label, and creates a
labelling CSV.
|
class |
ImageCSVLabeller |
class |
ImageLabeller<T>
Associates a label with an image.
|
class |
ImageLabellerStringMap<T>
Maps one set of labels to another
|
Modifier and Type | Class and Description |
---|---|
class |
ScaleImage<S>
Base class for tasks whose primary aim is to scale (resize) an image.
|
class |
ScaleImageCommonSize
Creates a scaled copy of images, ensuring all images have identical output size.
|
class |
ScaleImageIndependently
Creates a scaled copy of images, treating each image independently, and without any padding or
alignment.
|
Modifier and Type | Class and Description |
---|---|
class |
SegmentInstanceWithModel<T extends InferenceModel>
Using a model-pool, performs instance segmentation on an image producing zero, one or more
objects per image.
|
Modifier and Type | Class and Description |
---|---|
class |
ExtractSlice
Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice.
|
Modifier and Type | Class and Description |
---|---|
class |
BackgroundSubtractor |
class |
WithFilterBase |
class |
WithRadiusBase
A
ChannelProviderUnary with a 'radius' parameter |
Modifier and Type | Class and Description |
---|---|
class |
EdgeFilterIJ |
class |
GaussianBlur2D |
Modifier and Type | Class and Description |
---|---|
class |
MeanFilter2D |
class |
VarianceFilter2D |
Modifier and Type | Class and Description |
---|---|
class |
MedianFilter2D |
class |
MedianFilter3D |
Modifier and Type | Class and Description |
---|---|
class |
AddEdgeFilters |
Modifier and Type | Class and Description |
---|---|
class |
FillHoles |
class |
MorphologicalOperation
Applies an ImageJ (2D) morphological operation to each slice
|
Modifier and Type | Class and Description |
---|---|
class |
DrawLineAlongConvexHull
Draws a lines between successive points on the convex-hull of an object.
|
Modifier and Type | Class and Description |
---|---|
class |
FloodFillEachIntensityLevel
Creates an object for each separate intensity-value (beginning at
startingColor ) by
flood-filling. |
Modifier and Type | Class and Description |
---|---|
class |
MontageSlices |
Modifier and Type | Class and Description |
---|---|
class |
ThresholderSimpleFillHoles2D |
Modifier and Type | Class and Description |
---|---|
class |
Autoname
Names of the channels from the metadata if it exists, or after RGB, or by index.
|
class |
FromEntries |
class |
FromMetadata |
class |
SingleChannel
For an image with a single channel
|
Modifier and Type | Class and Description |
---|---|
class |
Bytewise
Makes a simple bytewise copy of a file, where no byte is changed.
|
class |
CompressAnyTIFF
Create a voxelwise compressed copy of any TIFF file being copied, and otherwise do a
Bytewise copy. |
class |
CopyFilesMethod
A method used for copying files (e.g.
|
Modifier and Type | Class and Description |
---|---|
class |
Anonymize
Copies files to a number
001, 002 etc. |
class |
CopyFilesNaming<T>
How an output name (and path) is selected for an input file when copying.
|
class |
CopyFilesNamingOne |
class |
CopyFilesNamingWithoutSharedState
Base class for implementations of
CopyFilesNaming where each file is copied independently
of the others. |
class |
FilterWithRegularExpression
Rejects files that fail to match a particular regular-expression
|
class |
OutputPrefixWithExtension
Copies files using whatever prefix is assigned to an input by the
OutputManager as the
file-name, adding the same extension as the source file. |
class |
PreserveName
Copies files to maintain the same relative-path from the destination file to the
destination-directory, as existed from the source file to the source-directory.
|
class |
RegularExpressionBase
A base class for
CopyFilesNaming classes that use a regular-expression. |
class |
RemoveWhitespace
Removes any whitespace characters from the path
|
class |
SubstituteRegularExpression
A regular expression substitution (replaceAll) is applied to the relative-path
|
Modifier and Type | Class and Description |
---|---|
class |
ClusterByTimestamp
Associates particular timestamp with each file, and clusters.
|
Modifier and Type | Class and Description |
---|---|
class |
GroupFiles
An
InputManagerWithStackReader that can unify separate images in separate files to form a
single Stack . |
Modifier and Type | Class and Description |
---|---|
class |
AtLeastZSlices |
class |
CheckParsedFilePathBag |
Modifier and Type | Class and Description |
---|---|
class |
FilePathParser |
class |
RegularExpression |
Modifier and Type | Class and Description |
---|---|
class |
FromOutputName |
class |
IfRelativeToDirectory
Multiplexes between two namers depending on if the relative-to-directory option is
selected.
|
class |
LastDirectories
Derives a name by taking the filename together with optionally several subdirectories names.
|
class |
NormalizedPath
Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
|
class |
RegExMatcher |
class |
RelativeToDirectory
Constructs a name by finding the relative-path between the file and the input-directory.
|
class |
RemoveExtension
Removes extensions from the identifier (but not from the file) and only if the extension
hasn't already been removed upstream.
|
class |
SubsetRangeIfRequested
If specified in the context, the existing name if subsetted according to an index range.
|
Modifier and Type | Class and Description |
---|---|
class |
PatternSpan
Finds a pattern in the file-path, and uses a portion of the file-path in that pattern to form the
name.
|
Modifier and Type | Class and Description |
---|---|
class |
FilePath |
class |
RootedFilePath |
class |
StaticFilePath |
Modifier and Type | Class and Description |
---|---|
class |
DirectoryStructure
Reuses the directories between a path and its root to form the output - and also the filename.
|
class |
FromDescriptiveName
The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create
an output prefix.
|
class |
HomeSubdirectory |
class |
IfIncrementingNumberRequested
Multiplexes between two
PathPrefixer s depending on whether an incrementing number
sequence was output was requested. |
class |
LastDirectoryAsPrefix
Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
|
class |
PathRegEx
Matches a regex against incoming file-paths to form a prefix for output
|
Modifier and Type | Class and Description |
---|---|
class |
TimestampPattern
Extracts a timestamp from a file-name if it exists.
|
Modifier and Type | Class and Description |
---|---|
class |
Combine |
class |
FileSetFromStringSet |
class |
Limit |
class |
LimitWithDirectory |
class |
RandomOrder |
class |
RemoveMatching |
class |
SampleWithDirectory |
class |
SortAlphabetically |
class |
SortAlphabeticallyWithDirectory |
Modifier and Type | Class and Description |
---|---|
class |
IfGroupIndexRange
When a
IndexRangeNegative is passed as an argument, an InputGrouper is
constructed that extracts elements from a Path . |
class |
RemoveLastElement
Splits an identifier into elements by the directory separator, and removes the final element.
|
Modifier and Type | Class and Description |
---|---|
class |
BranchIfDebug<T extends InputFromManager>
Uses one input-manager normally, but a different one if in debug mode.
|
class |
Exclude<T extends InputFromManager>
Excludes all inputs whose identifiers match a regular expression.
|
class |
LimitIfRequested<T extends InputFromManager>
Like
Limit if it is requested in the InputContextParameters , makes no change to
the inputs. |
class |
ShuffleIfRequested<T extends InputFromManager>
Like
Shuffle if requested in the InputContextParameters otherwise makes no change
to the inputs. |
Modifier and Type | Class and Description |
---|---|
class |
NamedChannels
An image viewed as a set of channels, each with a unique name.
|
class |
NamedChannelsAppend |
class |
NamedChannelsBase
Parent for all the
NamedChannels classes |
Modifier and Type | Class and Description |
---|---|
class |
NamedFiles
Implementation of
NamedFilesBase that is an InputManager that accepts FileInput as input and derives a name. |
class |
NamedFilesBase<T extends InputFromManager>
Base class for an
InputManager that produces inputs that are created from a NamedFile . |
class |
NamedFilesWithDirectory
|
Modifier and Type | Class and Description |
---|---|
class |
DirectoryDepth
Lists all directories to a certain depth
|
class |
FilterForExistingFiles |
Modifier and Type | Class and Description |
---|---|
class |
FilterCSVColumn<T extends InputFromManager>
Finds a CSV file with the names of an input as the first-column.
|
class |
FilterDescriptiveName<T extends InputFromManager>
Filters all the input objects for only those with certain types of descriptive-names.
|
class |
FilterIfDebug<T extends InputFromManager>
Filters a list of inputs when in debug-mode
|
Modifier and Type | Class and Description |
---|---|
class |
ConvertNamedChannelsToStack
Manager that converts (one channel)
NamedChannelsInput to StackSequenceInput . |
class |
Stacks
An
InputManager where each file provides one or more
Stack s. |
Modifier and Type | Class and Description |
---|---|
class |
BMP
The headers found in a BMP file.
|
class |
HeaderFormat
Populates
ImageMetadata from the header of an image-file. |
class |
JPEG
The headers found in a JPEG file.
|
class |
PNG
The headers found in a PNG file.
|
Modifier and Type | Class and Description |
---|---|
class |
AlwaysReject
A special
ImageMetadataReader that will always throw an exception and reject a file. |
class |
InferFromHeader
Tries to construct the
ImageMetadata from EXIF and other metadata, if available, or
otherwise falls back to another reader. |
Modifier and Type | Class and Description |
---|---|
class |
CollapseFileName
Removes the file-name from a path, but keeps the directories and preserves the file-extension.
|
class |
Constant
Always generates a constant path irrespective of the the input
|
class |
InsertRegExGroups
Generates an out string where $digit$ is replaced with the #digit group from a regex
|
class |
JoinRegExGroups
Generates an outstring of the form
|
class |
RemoveTrailingDirectory |
class |
Replace
Generates a file-path by replacing all occurrences of a string-pattern with another
|
class |
Rooted |
Modifier and Type | Class and Description |
---|---|
class |
BranchExtension
If the extension(s) of a path matches a particular value, then use a particular reader, otherwise
a fallback.
|
class |
FlattenAsChannel
Combines all series and frames returned by a reader by converting them into multiple channels in
the same image.
|
class |
ImposeResolution
Adds an explicit
Resolution to an image after it has been read. |
class |
MultiFileReader |
class |
ReadVoxelExtentXml
Reads
Resolution from an XML file associated an image. |
class |
RejectIfConditionXYResolution
If the XY resolution of an opened-image meets a certain condition then the resolution is scaled
by a factor.
|
class |
RotateImageToMatchEXIFOrientation
Rotates an image to match any EXIF orientation information, if it exists.
|
Modifier and Type | Class and Description |
---|---|
class |
BranchChannels
Uses different raster-writers depending on the number/type of channels.
|
class |
BranchStack
Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly
3D.
|
class |
BranchSuggestedFormat
Selects particular writers based on if particular suggested image formats are present.
|
class |
ImageIOWriter |
class |
StackWriterDelegateBase
A base class for a
StackWriter delegates to another StackWriter based on values
of a StackWriteAttributes . |
class |
WriteResolutionXml
When writing a stack, an additional file is written to indicate the physical voxel sizes, if this
information is known.
|
Modifier and Type | Class and Description |
---|---|
class |
Summarizer<T>
Summarizes a set of elements by outputting a descriptive string.
|
class |
SummarizerAggregate<T>
Collects summary data about a set of input files that will eventually be outputted to the user
|
class |
SummarizerCount<T>
A count of the number of inputs.
|
class |
SummarizerListMultiline<T>
Creates a string where each line is an element.
|
class |
SummarizerSplitMoreThan<T>
Multiplexes between two summarizers depending on the total number of count.
|
Modifier and Type | Class and Description |
---|---|
class |
BitDepth |
class |
ImageSize
Summarizes the size of images.
|
class |
SummarizerImageMetadata<T>
Summarizes
ImageMetadataInput in different ways. |
class |
SummarizerImageMetadataSimple<T>
A simple summarizer, where there's one summary-item per image.
|
Modifier and Type | Class and Description |
---|---|
class |
ExtractIdentifier<T extends InputFromManager>
Extracts the identifier from an
InputFromManager to summarize further. |
class |
ExtractIdentifierAndPath<T extends InputFromManager>
Extracts the identifier and path from an
InputFromManager to summarize further. |
class |
ExtractPath<T extends InputFromManager>
Extracts a
Path from an input to summarize further. |
class |
SummarizerInputFromManager<T extends InputFromManager,S>
Extracts a particular item from an
InputFromManager for further summarization downstream. |
Modifier and Type | Class and Description |
---|---|
class |
ExtensionCount
Remembers each unique extension, and associated count
|
class |
FilePathPattern
Converts a list of file-paths into a form that tries to find a pattern in the naming style using
the path-pattern-finder library.
|
class |
FileSizeStatistics
Tracks the range of file-size.
|
class |
SummarizerPath
Base class for
Summarizer s that operate on the Path associated with inputs. |
Modifier and Type | Class and Description |
---|---|
class |
CombineCSV
Combines multiple CSV files into a single CSV file.
|
class |
CopyFiles<T>
Copy files to the output-directory, possibly changing the name or performing other operations
like compression in the process.
|
class |
SummarizeBase<T extends InputFromManager,S> |
class |
SummarizeInputs<T extends InputFromManager> |
Modifier and Type | Class and Description |
---|---|
class |
FeatureListProviderLDAClassifier<T extends FeatureInput> |
class |
FeatureListProviderSVMClassifier |
Modifier and Type | Class and Description |
---|---|
class |
MergeSpatialClusters
Merges spatially-adjacent objects using the DBScan clustering algorithm.
|
Modifier and Type | Class and Description |
---|---|
class |
AddCriteriaFeatureRelationThreshold |
Modifier and Type | Class and Description |
---|---|
class |
MarkBoundsDefine |
class |
MarkBoundsReference |
Modifier and Type | Class and Description |
---|---|
class |
AndList |
class |
AnySliceCenterOnMask
The center ps of at least one slice should be on the stack Tries overall center point first, and
then projects it onto each slice
|
class |
CenterOnMask |
class |
CheckMarkWithMask |
class |
FeatureValueCheckMark<T extends FeatureInput> |
class |
FeatureValueIndividualEnergyGreaterThan |
class |
FeatureValueMarkGreaterEqualThan |
class |
Not |
class |
RadiiMinRatio |
class |
VolumeMin |
Modifier and Type | Class and Description |
---|---|
class |
TraverseOuterContourOnImage
Implementation of
TraverseOuterCounter that uses a VisitScheduler for determining
which pixels are traversed. |
class |
TraverseOuterCounter
Traverses the pixels on the exterior outer contour of an
ObjectMask . |
Modifier and Type | Class and Description |
---|---|
class |
VisitScheduler |
class |
VisitSchedulerAnd |
class |
VisitSchedulerConvexAboutRoot |
class |
VisitSchedulerMaxDistanceAlongContour |
class |
VisitSchedulerUniformSample |
Modifier and Type | Class and Description |
---|---|
class |
DefineOutputterWithEnergy
Like a
Define but outputs also an energy-stack. |
class |
VisualizeOnBackground
Adds a visualization for all binary-masks and object-collections that are added using a
particular background
|
Modifier and Type | Class and Description |
---|---|
class |
FromMarks
Creates object-masks from a
MarkCollection where (a particular region of) each mark
creates an object. |
Modifier and Type | Class and Description |
---|---|
class |
FromMarkProposer |
class |
FromProvider |
class |
FromSerializedMarks |
Modifier and Type | Class and Description |
---|---|
class |
ChooseOneList |
class |
FromSerializedObject |
class |
MarkProposerFromList |
class |
MarkProposerReference |
class |
MarkProposerUnary |
class |
ObjectAsPoints |
class |
OrderedList |
class |
OrientationAndRadiiProposer
Proposes both an orientation and radii for a
ConicBase |
class |
Position |
Modifier and Type | Class and Description |
---|---|
class |
Check |
class |
MarkFromCollectionProposerUnary |
class |
UniformRandom |
Modifier and Type | Class and Description |
---|---|
class |
MarkMergeProposerReference |
class |
MergeMarkEllipse |
Modifier and Type | Class and Description |
---|---|
class |
RandomOrientation |
class |
RandomXY |
Modifier and Type | Class and Description |
---|---|
class |
IncludeRandomObjects
1.
|
class |
XYOrientationExtendToZ |
Modifier and Type | Class and Description |
---|---|
class |
FindPointOnContour
Finds a pixel in a particular direction on the exterior outer contour of an object.
|
class |
FindPointOnContourWalk
Walks incrementally in a particular direction until the contour is found.
|
Modifier and Type | Class and Description |
---|---|
class |
MergeLists |
class |
PointsFromOrientationProposer |
class |
TraversePointsOnContour |
Modifier and Type | Class and Description |
---|---|
class |
RadiiProposerRepeat |
class |
UniformRandomRadiiProposer |
Modifier and Type | Class and Description |
---|---|
class |
FromUnitValueDistance |
class |
GaussianSampler
Samples from a Gaussian distribution whose parameters are determined by a
Dictionary . |
Modifier and Type | Class and Description |
---|---|
class |
MarkSplitProposerReference |
Modifier and Type | Class and Description |
---|---|
class |
FromSingleMark |
class |
PointsFromObjects |
class |
ReferenceOrEmpty
Returns an existing marks-collection or an empty set if it doesn't exist
|
Modifier and Type | Class and Description |
---|---|
class |
CreateEllipse |
class |
RequireFeatureRelationThreshold |
class |
RetrieveSingleMarkOnly
Retrieves a mark from a marks, assuming there is only one mark in a marks, otherwise throwing an
exception
|
Modifier and Type | Class and Description |
---|---|
class |
AllSlicesMaskEverythingNonZero
Only considers voxels with non-zero intensity.
|
class |
AllSlicesMaskNonZero
Gets all slices where indexNonZero has at least one non-zero pixel in that slice
|
class |
CenterSlice |
class |
CenterSliceBase |
class |
CenterSliceWindow
Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one
slice, specifically centerSlice+- windowSize
|
class |
GreatestAreaSlice |
class |
IndexedRegionBase
MarkRegion with a region and an index |
class |
MaxNonZero |
class |
SelectSlicesBase |
class |
SelectSlicesWithIndexBase |
class |
Specific |
class |
Thresholded |
Modifier and Type | Class and Description |
---|---|
class |
SegmentThresholdAboveMinBound |
Modifier and Type | Class and Description |
---|---|
class |
ColoredMarks
Draws a colored representation (outline or filled) of an
MarkCollection on a background |
Modifier and Type | Class and Description |
---|---|
class |
ConvertNamedChannels<T extends NamedChannelsInput,S,U extends InputFromManager>
Converts
NamedChannelsInput to a variety of others to match a delegate task. |
Modifier and Type | Class and Description |
---|---|
class |
Develop
Derives various types of outputs (images, histograms etc.) from
MultiInput s. |
Modifier and Type | Class and Description |
---|---|
class |
ExportReportFeatures
Creates a report of feature values from a
DefineOutputter and a MultiInput . |
Modifier and Type | Class and Description |
---|---|
class |
FromObjects<T extends FeatureInput>
Extracts features for each object in a collection.
|
Modifier and Type | Class and Description |
---|---|
class |
ExportObjectsAsCroppedImages
Exports a cropped image for each object-mask showing its context within an image
|
class |
ExportObjectsBase<T extends InputFromManager,S> |
class |
ExportObjectsFromCSV
Given a CSV with a point representing one or more object-masks, these object-masks are extracted
from a segmentation.
|
class |
FromCSVInputManager |
Modifier and Type | Class and Description |
---|---|
class |
ColumnDefinition |
class |
Pairwise |
class |
Single |
Modifier and Type | Class and Description |
---|---|
class |
SegmentMarksFromImage
Segments an image into a collection of
Mark s. |
Modifier and Type | Class and Description |
---|---|
class |
DotProductOrientationToVector |
class |
EllipsoidAxisRatio |
class |
EllipsoidMaxAreaIntersectingPlane |
class |
FeatureMarkDirection |
Modifier and Type | Class and Description |
---|---|
class |
EccentricityAxisAligned |
class |
MaxRatioRadii |
class |
OrderedRadius |
class |
RadiiRatio |
Modifier and Type | Class and Description |
---|---|
class |
BoundingBoxExtent |
class |
FeatureMarkRegion |
class |
MarkEllipseCircumEstimate
Estimates the circumference of an ellipse based upon finding the area of the shell, and dividing
// by the shell
|
class |
Volume |
Modifier and Type | Class and Description |
---|---|
class |
AsCollection |
class |
AsSingleMark |
class |
CoefficientOfVarianceFromAll |
class |
MeanFromAll |
class |
NumberMarks |
Modifier and Type | Class and Description |
---|---|
class |
AsMark |
class |
AsObject |
class |
BBoxRatio |
class |
FeatureSingleMemoRegion |
class |
Intensity |
class |
MaxSliceArea |
class |
MeanIntensityDifference |
class |
Size |
class |
SurfaceSizeMaskNonZero |
Modifier and Type | Class and Description |
---|---|
class |
FeatureAsIndividualProportionate
Calculates each feature individually, and combines them using the ratios between
itemProportionate as weights
|
class |
FeaturePairMemoOne |
class |
FeaturePairMemoSingleRegion |
class |
MinFeatureAsIndividual |
Modifier and Type | Class and Description |
---|---|
class |
BoundingBoxZDistance
Measures the amount of distance in Z for the bounding box.
|
class |
BoundingBoxZOverlapRatio
Measures the amount of bounding box overlap in the Z dimension
|
class |
MinimumDistanceByDimension
The minimum distance in any one particular axis-aligned direction (i.e.
|
Modifier and Type | Class and Description |
---|---|
class |
MaxOverlapRatio |
class |
OverlapMaskBase |
class |
OverlapMIPBase |
class |
OverlapNumberVoxelsMask |
class |
OverlapNumVoxels |
class |
OverlapRatio |
class |
OverlapRatioMask |
Modifier and Type | Class and Description |
---|---|
class |
UnitConverter
Converts units (distance, area, volume) to a another representation (e.g.
|
Modifier and Type | Class and Description |
---|---|
class |
Geometry |
class |
NoAnnealing |
Modifier and Type | Class and Description |
---|---|
class |
KernelBirthPartition
Proposes new marks ONLY if they haven't already been proposed and accepted.
|
class |
KernelDeathPartition |
class |
KernelReplacePartition |
Modifier and Type | Class and Description |
---|---|
class |
KernelBirth<T>
Adds a new mark (a "birth") to create a proposal.
|
class |
KernelBirthAndKill |
class |
KernelDeath<T> |
class |
KernelExchange |
class |
KernelInitialMarksFromPartition |
class |
KernelInitialMarksProposed |
class |
KernelInitialMarksVoxelized |
class |
KernelMerge |
class |
KernelReplace<T> |
class |
KernelSplit |
Modifier and Type | Class and Description |
---|---|
class |
KernelBirthVoxelized
As an example, this is like sampling with replacement.
|
class |
KernelDeathVoxelized |
Modifier and Type | Class and Description |
---|---|
class |
KernelProposerOptionDual<T,S> |
class |
KernelProposerOptionSingle<T,S> |
Modifier and Type | Class and Description |
---|---|
class |
SegmentWithMarkedPointProcess
Segments a channel with a Marked
Point Process.
|
Modifier and Type | Class and Description |
---|---|
class |
AddDualTransformer |
class |
RetrieveDestinationFromDual |
class |
RetrieveSourceFromDual |
Modifier and Type | Class and Description |
---|---|
class |
RemovePartition |
class |
RemovePartitionAndThen<T> |
Modifier and Type | Class and Description |
---|---|
class |
AddEnergy |
class |
RetrieveDestinationFromVoxelized<T> |
class |
RetrieveSourceFromVoxelized<T> |
class |
VoxelizeWithTransform<T>
Converts a Marks to a MarksToPixelized using a transformer
|
Modifier and Type | Class and Description |
---|---|
class |
ConstantWeight
All marks have weight of 1
|
class |
ExtractWeightFromMark |
class |
NumberPoints |
Modifier and Type | Class and Description |
---|---|
class |
FromDualVoxelizedMarks |
class |
FromVoxelizedMarksWithEnergy |
class |
ToPixelizedExtracter<T> |
Modifier and Type | Class and Description |
---|---|
class |
KernelStateBridge<U,T>
Transforms a kernel-to-state and vice versa.
|
class |
KernelStateBridgeIdentity<T>
No transformation occurs as Kernel and State are the same type
|
class |
KernelStateBridgePixelize<T>
State derived from the kernel takes the form of
ToPixelized<T> |
class |
KernelStateBridgeTransformer<U,T> |
Modifier and Type | Class and Description |
---|---|
class |
AssignMode<S,T,U>
How assignments and other decisions are made in the SimulatedAnnealing optimizaton
|
class |
DirectAssignMode<S>
Directly assigns a state for every optimisation step
|
class |
TransformationAssignMode<S,T,U>
Applies a transformation to the kernel-type U to calculate the Energy used as the primary readout
during optimization
|
Modifier and Type | Class and Description |
---|---|
class |
ConsoleAccepted |
class |
ConsoleAggregatedReporter |
class |
CSVReporterAggregated
Outputs statistics on current energy / kernel acceptance etc.
|
class |
CSVReporterBest
Outputs a CSV with statistics on the configuration/energy only the best
configuration state changes.
|
class |
KernelIterDescriptionSerializerPeriodicReporter |
class |
Log4JReporter |
class |
MemoryUsageReporter |
class |
MinimalExecutionTimeStatsReporter |
class |
NullReporter<T>
Dummy reporter that takes no action.
|
class |
ObjectSerializerPeriodicReporter<T extends Serializable> |
class |
OptimizationStepLogReporter |
class |
TextFile |
class |
TextFileMarksReporter |
class |
VoxelizedMarksChangeReporter |
class |
VoxelizedMarksPeriodicReporter |
Modifier and Type | Class and Description |
---|---|
class |
SimulatedAnnealing<S,T,U>
Finds an optima using a simulated-annealing approach
|
class |
UniformProposal<S,V>
Repeatedly propose new collections of marks and take the collection with optimal energy.
|
Modifier and Type | Class and Description |
---|---|
class |
StateReporterIdentity<T>
Assumes the state is reported without any transformation
|
class |
StateReporterToPixelized<T>
Assumes we are interested in
VoxelizedMarksWithEnergy as reporting type, and our
optimization-state is in the form ToPixelized<T> |
class |
StateReporterTransformer<T,S> |
Modifier and Type | Class and Description |
---|---|
class |
NumberIterations
Terminates after a specific number of iterations.
|
class |
NumberIterationsBase
Parent class for a
TerminationCondition where the number-of-iterations is a bean-field. |
class |
UnchangedBase
Parent class for
TerminationCondition that rely on some attribute remaining unchanged for
a certain number of iterations. |
class |
UnchangedScore
Terminate when the score remains unchanged for a certain number of iterations.
|
class |
UnchangedSize
Terminate when the size remains unchanged for a certain number of iterations.
|
Modifier and Type | Class and Description |
---|---|
class |
DecodeMaskRCNN
Decodes the inference output from a Mask-RCNN implementation.
|
Modifier and Type | Class and Description |
---|---|
class |
DecodeEAST
Extracts text from a RGB image by using the EAST deep neural network model and the ONNX
Runtime.
|
Modifier and Type | Class and Description |
---|---|
class |
SegmentObjectsFromONNXModel
Performs instance-segmentation using the ONNX Runtime and an
.onnx model file. |
Modifier and Type | Class and Description |
---|---|
class |
ColorConverterBase
Converts a RGB stack into another color space using OpenCV.
|
class |
ConvertRGBToHSV
Converts a RGB image to the HSV color
space.
|
class |
ConvertRGBToLab
Converts a RGB image to the Lab color
space.
|
Modifier and Type | Class and Description |
---|---|
class |
HOGDescriptor
Creates the entire HOG descriptor for an image.
|
class |
HOGFeature
One part of a Histogram
of Oriented Gradients descriptor, as applied to an image stack.
|
class |
HOGParameters
Parameters for calculating a HOG Descriptor covering window-size, block-size etc.
|
Modifier and Type | Class and Description |
---|---|
class |
OpenCV
Interpolation using OpenCV for resizing an image.
|
Modifier and Type | Class and Description |
---|---|
class |
SegmentObjectsFromTensorFlowModel
Performs instance-segmentation using OpenCV's DNN module and a TensorFlow
.pb SavedModel file. |
Modifier and Type | Class and Description |
---|---|
class |
OpenCVReader
Reads a stack from the file-system using OpenCV.
|
class |
OpenCVWriter
Writes a stack to the file-system using OpenCV and a specified extension.
|
Modifier and Type | Class and Description |
---|---|
class |
FromDictionary<T extends FeatureInputDictionary>
Extracts a key-value from a
Dictionary as a double. |
class |
WithValueBase<T extends FeatureInput>
Operations that use a specified constant value
|
Modifier and Type | Class and Description |
---|---|
class |
AbsoluteValue<T extends FeatureInput> |
class |
AddConstantTo<T extends FeatureInput> |
class |
ConstantToThePowerOf<T extends FeatureInput> |
class |
Divide<T extends FeatureInput> |
class |
DivideByConstant<T extends FeatureInput> |
class |
InvertedMax<T extends FeatureInput>
Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
|
class |
Multiply<T extends FeatureInput> |
class |
MultiplyByConstant<T extends FeatureInput> |
class |
SubtractFrom<T extends FeatureInput> |
class |
ToThePowerOfConstant<T extends FeatureInput> |
Modifier and Type | Class and Description |
---|---|
class |
IfCondition<T extends FeatureInput>
The result of featureCondition is compared to a threshold, and then either the underlying feature
is calculated (positive case), or featureElse is (negative case)
|
Modifier and Type | Class and Description |
---|---|
class |
Maximum<T extends FeatureInput> |
class |
Mean<T extends FeatureInput>
Arithmetic mean of a list of features
|
class |
MeanGeometric<T extends FeatureInput> |
class |
Minimum<T extends FeatureInput> |
Modifier and Type | Class and Description |
---|---|
class |
CompareWithRange<T extends FeatureInput>
Compares a value with a range, returning specified constants if its inside the range, below it or
above it
|
class |
CompareWithRangeFeature<T extends FeatureInput>
Like
CompareWithRange but uses features to calculate boundary values |
class |
IfConditionWithinRange<T extends FeatureInput>
Calculates a value if a condition lies within a certain range, otherwise returns constants
|
class |
IfOutsideRange<T extends FeatureInput>
Clamps a value if it lies outside the range - instead returning particular constants if below or
above an acceptable range
|
class |
NormalizedRange<T extends FeatureInput>
The range of two feature values (i.e.
|
class |
Range<T extends FeatureInput>
The statistical range between two values i.e.
|
class |
RangeCompareBase<T extends FeatureInput> |
class |
RangeCompareFromScalars<T extends FeatureInput>
A base-class for setting the boundaries of the range using constant scalars
|
Modifier and Type | Class and Description |
---|---|
class |
ReplaceInfinity<T extends FeatureInput> |
class |
ReplaceNaN<T extends FeatureInput> |
class |
ReplaceUnusualValue<T extends FeatureInput>
Calculates the underlying feature, but replaces the result with a constant if it happens to be an
"unusual" value
|
Modifier and Type | Class and Description |
---|---|
class |
GaussianCumulative<T extends FeatureInput> |
class |
StatisticalBase<T extends FeatureInput>
Calculates a score based upon the statistical mean and std-deviation.
|
class |
ZScore<T extends FeatureInput> |
Modifier and Type | Class and Description |
---|---|
class |
ConvertUnits<T extends FeatureInput> |
Modifier and Type | Class and Description |
---|---|
class |
FitPoints |
class |
FitPointsFromObjects |
class |
SplitContourAtSaddlePoints
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn"
points.
|
Modifier and Type | Class and Description |
---|---|
class |
ConvexHull2D
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
|
class |
ConvexHull3D |
class |
ConvexHullBase |
Modifier and Type | Class and Description |
---|---|
class |
AxisRatioEllipsoid |
class |
EllipsoidBase |
class |
Ellipsoidicity |
class |
Ellipticity |
Modifier and Type | Class and Description |
---|---|
class |
ConicFitterBase |
class |
LinearLeastSquaresEllipseFitter
Fits a set of points to an ellipse using a linear least squares method.
|
class |
LinearLeastSquaresEllipsoidFitter
Fits an ellipsoid to points using a linear least squares approach
|
class |
LinearLeastSquaresViaNormalEquationBase |
class |
PointsFitterToMark |
class |
ReflectInAxesWithinDistance
Reflects points in each axes if all points are within a certain distance from it
|
Modifier and Type | Class and Description |
---|---|
class |
QuickExperiment<S>
A quick way of defining an
InputOutputExperiment where several assumptions are made. |
class |
QuickMultiDatasetExperiment<T extends InputFromManager,S>
Makes a lot of assumptions, that allows us to reduce the number of inputs to an
InputOutputExperiment . |
Modifier and Type | Class and Description |
---|---|
class |
AdjacentFile |
class |
MultiInputManagerQuick
A multi-input manager that makes various assumptions, so it can be more quickly specified.
|
class |
NamedChannelsQuick
A particular type of NamedChannels which allows easier input of data, making several assumptions.
|
class |
QuickBase<T extends InputFromManager>
A base for quick managers that make various assumptions about file-structure.
|
Modifier and Type | Class and Description |
---|---|
class |
AppendCsv
A CSV that is appended from the root of a project
|
class |
AppendDictionary |
class |
AppendFilePath |
class |
AppendHistogram |
class |
AppendMarks |
class |
AppendObjects |
class |
AppendStack
A stack from a stack-collection
|
class |
AppendStackDirect
A stack from a stack-collection
|
class |
FilePathAppendBase |
class |
FilePathBaseAppendToManager |
class |
FilePathBaseAppendToManagerWithFileID |
class |
MatchedAppendCsv
An append CSV and corresponding match value
|
Modifier and Type | Class and Description |
---|---|
class |
ExperimentResultsExperimentStructure
Finds some files produced in a previous experiment assuming a certain structure
|
class |
ExperimentStructure
A
PathPrefixer that combines a prefix with an experimentType . |
class |
QuickMultiDatasetStructuredExperiment<T extends InputFromManager,S>
Similar to
QuickMultiDatasetStructuredExperiment put sets properties according to an
expected directory structure. |
class |
RootedExperiment |
Modifier and Type | Method and Description |
---|---|
static <T extends AnchorBean<?>> |
BeanTestChecker.check(T bean)
Checks if a bean has all necessary items, throwing a run-time exception if it does not.
|
Modifier and Type | Class and Description |
---|---|
class |
MockFeatureWithCalculation
A feature that returns the number-of-voxels in an object by using am internal mock-calculation.
|
Modifier and Type | Method and Description |
---|---|
static <T extends AnchorBean<?>> |
BeanInstanceMapFixture.check(T bean)
Checks if a bean has all necessary items, throwing a run-time exception if it does not.
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.