Package | Description |
---|---|
org.anchoranalysis.annotation.io.assignment |
A pairing of objects from two collections (bipartite matching).
|
org.anchoranalysis.annotation.io.bean.comparer |
What to compare an annotation (ground truth) against?
|
org.anchoranalysis.bean.permute |
Applying permutations to a bean's fields.
|
org.anchoranalysis.bean.shared |
Utility beans which have a generally broader use than a specific module.
|
org.anchoranalysis.image.bean.channel |
Base classes for performing operations on
Channel s. |
org.anchoranalysis.image.bean.displayer | |
org.anchoranalysis.image.bean.spatial.direction |
Beans to specify a direction.
|
org.anchoranalysis.image.core.bufferedimage |
Conversions and operations involving Java AWT's
BufferedImage . |
org.anchoranalysis.image.core.channel.factory |
Factory classes for creating
Channel for various
voxel data-types. |
org.anchoranalysis.image.core.dimensions |
Classes to describe the size of images or components of images both in voxels and physically.
|
org.anchoranalysis.image.core.object |
The key data entity
org.anchoranalysis.image.voxel.object and related-classes and
operations. |
org.anchoranalysis.image.core.object.label |
Labelling elements (object-masks or similar) with unique successive integers in a channel.
|
org.anchoranalysis.image.core.object.scale |
Scaling object-collections, or lists of elements with object-representations.
|
org.anchoranalysis.image.core.points |
Operations that extract points from image data entities or vice versa.
|
org.anchoranalysis.image.core.stack |
Defines the key data object,
Stack , and related
classes. |
org.anchoranalysis.image.io.bean.channel |
Beans pertaining to reading
Channel s as input. |
org.anchoranalysis.image.io.object.output.rgb |
Writing an
ObjectCollection to the filesystem as
RGB raster-images. |
org.anchoranalysis.image.io.stack |
Non-bean classes for reading / writing a
Stack from
and to the filesystem. |
org.anchoranalysis.image.voxel |
Data-structures to store and manipulate image raster-data or voxels.
|
org.anchoranalysis.image.voxel.binary |
The
BinaryVoxels class and related operations. |
org.anchoranalysis.image.voxel.convert.bufferedimage |
Converts anchor data-structures to the
BufferedImage used by Java's AWT. |
org.anchoranalysis.image.voxel.datatype |
The different data-types that can be used to represent voxels.
|
org.anchoranalysis.image.voxel.neighborhood |
A region in proximity to a voxel, encompassing this voxel as well as others.
|
org.anchoranalysis.image.voxel.object |
The fundamental data class that is an
ObjectMask
and related structures. |
org.anchoranalysis.image.voxel.object.morphological |
Morphological operations
applied to
ObjectMask s. |
org.anchoranalysis.io.bioformats |
Non-bean classes for filesystem I/O using Bioformats.
|
org.anchoranalysis.io.bioformats.copyconvert |
Converts the byte stream opened by Bioformats into channels of particular data-type.
|
org.anchoranalysis.io.input.bean.namer |
Beans to derive names (compact unique identifiers) from files.
|
org.anchoranalysis.mpp.bean.mark |
Beans generally related to
Mark s. |
org.anchoranalysis.mpp.feature.addcriteria |
Criteria for adding edges during optimization of marked-point-processes.
|
org.anchoranalysis.mpp.feature.bean.energy.scheme |
Creating
EnergyScheme s. |
org.anchoranalysis.mpp.feature.energy.scheme |
Factorized form of storing the energy during an energy-minimization optimization scheme.
|
org.anchoranalysis.mpp.io.input |
Non-beans for reading data structures related to marked point processes from the file system.
|
org.anchoranalysis.mpp.io.output |
Non-beans for writing data structures related to marked point processes from the file system.
|
org.anchoranalysis.mpp.overlay | |
org.anchoranalysis.mpp.segment.bean.define |
DefineOutputter and its sub-classes. |
org.anchoranalysis.mpp.segment.optimization |
Non-bean classes used in
org.anchoranalysis.mpp.segment.bean.optimization |
org.anchoranalysis.overlay |
Overlay s and related classes involving drawing entities on top
of an image. |
org.anchoranalysis.overlay.object |
An implementation of an
Overlay that draws an ObjectMask on an image. |
org.anchoranalysis.plugin.annotation.bean.comparison.assigner |
Pairs annotations from two different sets, creating an assignment of some type.
|
org.anchoranalysis.plugin.fiji.bean.mask.provider |
Implementations of
MaskProvider that use FIJI. |
org.anchoranalysis.plugin.image.bean.channel.convert |
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram . |
org.anchoranalysis.plugin.image.bean.mask.provider |
Implementations of
MaskProvider . |
org.anchoranalysis.plugin.image.bean.mask.provider.convert |
Implementations of
MaskProvider that convert
providers of other types to ObjectMask s. |
org.anchoranalysis.plugin.image.bean.mask.provider.segment | |
org.anchoranalysis.plugin.image.bean.stack.provider.color |
Implementations of
StackProvider that color
portions of an image. |
org.anchoranalysis.plugin.image.bean.thumbnail.stack |
Implementations of
ThumbnailFromStack . |
org.anchoranalysis.plugin.image.feature.bean.object.combine |
Features from combinations of
ObjectMask s. |
org.anchoranalysis.plugin.image.intensity.level |
Non-beans for calculating a thresholding level from itensity values.
|
org.anchoranalysis.plugin.image.task.bean.combine |
Combining multiple images together into a single image.
|
org.anchoranalysis.plugin.image.task.bean.feature.source |
Source of rows in feature-tables with
FeatureSource and derived classes. |
org.anchoranalysis.plugin.image.task.bean.grouped |
Tasks that involved stacks (usually each channel from an image) that are somehow
grouped-together.
|
org.anchoranalysis.plugin.image.task.bean.grouped.histogram |
Task(s) to export histograms of intensity values.
|
org.anchoranalysis.plugin.image.task.feature |
Non-bean classes pertaining to
Feature s as used in tasks. |
org.anchoranalysis.plugin.image.task.labeller |
Non-bean classes about labelling images.
|
org.anchoranalysis.plugin.image.task.segment |
Non-bean classes for image-segmentation.
|
org.anchoranalysis.plugin.image.task.stack |
Non-bean classes pertaining to stacks and channels as used in tasks.
|
org.anchoranalysis.plugin.image.thumbnail |
Non-bean classes for thumbnail creation.
|
org.anchoranalysis.plugin.io.bean.channel.map |
Implementations of
ChannelMapCreator . |
org.anchoranalysis.plugin.io.bean.file.copy.method |
Methods for copying files on the file-system.
|
org.anchoranalysis.plugin.io.bean.file.namer |
Implementations of
FileNamer . |
org.anchoranalysis.plugin.mpp.bean.region |
Implementations of
MarkRegion . |
org.anchoranalysis.plugin.mpp.bean.stack.provider |
Implementations of
StackProvider involving
Mark or related classes. |
org.anchoranalysis.plugin.mpp.experiment.bean.feature.source |
Implementations of
FeatureSource . |
org.anchoranalysis.plugin.mpp.experiment.objects.csv |
Reading rows from a CSV file.
|
org.anchoranalysis.plugin.mpp.segment.optimization |
Non-bean classes to help with optimization in
org.anchoranalysis.plugin.mpp.segment.bean.optimization and sub-packages. |
org.anchoranalysis.plugin.opencv.convert |
Conversion to/from OpenCV data-structures.
|
org.anchoranalysis.plugin.points.bean.fitter |
Fitting geometric structures to points.
|
org.anchoranalysis.plugin.points.calculate.ellipsoid |
CalculationPart related to fitting
ellipsoids to points by least-squares. |
org.anchoranalysis.plugin.points.convexhull |
Non-bean convex hull operations.
|
org.anchoranalysis.test.feature.plugins |
Testing utilities and fixtures with no greater downstream dependency than
anchor-image-feature or anchor-mpp.
|
Modifier and Type | Method and Description |
---|---|
static <T> CostMatrix<T> |
CostMatrix.create(List<T> first,
List<T> second,
boolean symmetric,
CheckedToDoubleBiFunction<T,T,CreateException> costCalculator)
Creates by calculating the cost between elements.
|
Modifier and Type | Method and Description |
---|---|
static <T> CostMatrix<T> |
CostMatrix.create(List<T> first,
List<T> second,
boolean symmetric,
CheckedToDoubleBiFunction<T,T,CreateException> costCalculator)
Creates by calculating the cost between elements.
|
Modifier and Type | Method and Description |
---|---|
List<NameValue<Stack>> |
MultipleComparer.createComparisonStacks(AnnotationWithMarks annotation,
DisplayStack background,
Path annotationPath,
ColorScheme colorScheme,
Path modelDirectory,
OperationContext context,
boolean debugMode)
|
Modifier and Type | Method and Description |
---|---|
<S> List<T> |
PermutedCopyCreator.createPermutedCopies(List<T> beans,
PermuteProperty<S> propertyToPermute,
PermutationAssigner setter)
Applies a permutation to a copy of each element in a list of beans, updating the custom name
of each bean to reflect the permutation.
|
Modifier and Type | Method and Description |
---|---|
Map<String,String> |
StringMap.create()
Derives a
Map representation for the mapping. |
Modifier and Type | Method and Description |
---|---|
abstract ChannelConverter<T> |
ConvertChannelTo.createConverter()
Creates the converter.
|
Modifier and Type | Method and Description |
---|---|
DisplayStack |
StackDisplayer.deriveFrom(Channel channel)
Creates from a
Channel . |
DisplayStack |
StackDisplayer.deriveFrom(RGBStack rgbStack)
Derives a
DisplayStack from a RGBStack . |
DisplayStack |
StackDisplayer.deriveFrom(Stack stack)
Derives a
DisplayStack from a RGBStack . |
Modifier and Type | Method and Description |
---|---|
DirectionVector |
AxisAlignedUnitVector.createVector() |
abstract DirectionVector |
DirectionVectorBean.createVector()
Creates a vector in a particular direction.
|
Modifier and Type | Method and Description |
---|---|
static BufferedImage |
BufferedImageFromStack.create(Stack stack)
Creates a
BufferedImage from a Stack . |
static BufferedImage |
BufferedImageFromStack.createRGB(Voxels<UnsignedByteBuffer> red,
Voxels<UnsignedByteBuffer> green,
Voxels<UnsignedByteBuffer> blue,
Extent extent)
Creates a
BufferedImage from three Voxels<UnsignedByteBuffer> representing
respectively, red, green, blue color components. |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFactory.createEmptyInitialisedToSupportMaxValue(Dimensions dimensions,
long maxIntensityValueNeeded)
Creates an empty initialized channel with discrete type with as minimal as needed data-type
to support a maximum value.
|
Constructor and Description |
---|
Resolution(double x,
double y,
double z)
Creates with a resolution from three double values for each dimension.
|
Resolution(Tuple3d tuple)
Constructs a resolution from a tuple.
|
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
ObjectFromPointsFactory.create(Collection<Point3i> points)
Create an
ObjectMask from a collection of points. |
static Histogram |
HistogramFromObjectsFactory.createFrom(Channel channel,
Mask mask)
|
static Histogram |
HistogramFromObjectsFactory.createFrom(Channel channel,
Optional<Mask> mask)
Creates a
Histogram of all voxel intensity values in channel , or only
those in mask if it is dfined. |
Modifier and Type | Method and Description |
---|---|
List<T> |
DecodeLabels.create(int smallVolumeThreshold)
Creates a list of elements from voxels that are labelled with unique integers (sequentially
increasing).
|
Map<T,T> |
DecodeLabels.create(Map<Integer,T> labelMap,
java.util.function.UnaryOperator<T> operationAfterScaling)
Creates a map of elements to other elements that are labelled with unique integers
(sequentially increasing) in voxels.
|
Channel |
LabelObjects.createLabelledChannel(BoundedList<T> elements,
Optional<Map<Integer,T>> mapLabels)
Creates a channel that contains a unique integer (label) for each element's
object-representation.
|
void |
LabelObjects.labelElements(Channel channel,
Iterable<T> elements,
Optional<Map<Integer,T>> mapLabels)
Replaces the contents of the channel so that all element's voxels are labelled with
successive unique integer identifiers 1,2,3 etc.
|
Constructor and Description |
---|
ScaledElements(List<T> elements,
ScaleFactor scaleFactor,
ObjectScalingMethod scalingMethod,
Optional<java.util.function.UnaryOperator<T>> preOperation,
Optional<java.util.function.UnaryOperator<T>> postOperation,
AccessObjectMask<T> access)
Creates elements to be scaled.
|
Modifier and Type | Method and Description |
---|---|
static List<Point2i> |
PointsFromMask.listFrom2i(Mask mask)
|
static List<Point2i> |
PointsFromObject.listFrom2i(ObjectMask object)
A list of two-dimensional integer points from the entire object-mask.
|
static List<Point2i> |
PointsFromObject.listFromOutline2i(ObjectMask object)
A list of points as three-dimensional integers from the outline of an object-mask
|
Modifier and Type | Method and Description |
---|---|
DisplayStack |
DisplayStack.extractSlice(int z)
Extract a particular z-slice from the
DisplayStack as a new stack, applying any
applicable conversion. |
Constructor and Description |
---|
DisplayStack(Stack stack,
boolean eventuallyThree,
java.util.function.Function<VoxelDataType,ChannelConverterAttached<Channel,UnsignedByteBuffer>> createConverter)
Create for a particular
Stack that may needed to be converted. |
Stack(boolean rgb,
Channel... channels)
Creates from a varying number of channels, and a flag to indicate if they represent an RGB
image or not.
|
Stack(Dimensions dimensions,
ChannelFactorySingleType factory,
int numberChannels,
boolean rgb)
Create with a particular number of empty
Channel s. |
Modifier and Type | Method and Description |
---|---|
abstract ChannelMap |
ChannelMapCreator.create(OpenedImageFile openedFile,
Logger logger)
Creates the
ChannelMap . |
Modifier and Type | Method and Description |
---|---|
protected RGBStack |
DrawCroppedObjectsGenerator.generateBackgroundRegion(ObjectCollectionWithProperties objects,
io.vavr.control.Either<Dimensions,DisplayStack> background) |
protected abstract RGBStack |
ObjectsAsRGBGenerator.generateBackgroundRegion(ObjectCollectionWithProperties objects,
io.vavr.control.Either<Dimensions,DisplayStack> background)
Creates a
RGBStack containing the background, without objects being drawn upon it. |
protected ObjectCollectionWithProperties |
DrawCroppedObjectsGenerator.generateMasks(ObjectCollectionWithProperties objects) |
protected abstract ObjectCollectionWithProperties |
ObjectsAsRGBGenerator.generateMasks(ObjectCollectionWithProperties objects)
Creates a
ObjectCollectionWithProperties indicative of the masks that will be imposed
on top of the background-region. |
Modifier and Type | Method and Description |
---|---|
static RGBStack |
ConvertStackToRGB.convert(Stack stack,
StackDisplayer displayer,
boolean alwaysNew)
Converts all of a
DisplayStack to a RGBStack . |
Modifier and Type | Method and Description |
---|---|
BoundedVoxels<T> |
BoundedVoxels.region(BoundingBox box,
boolean reuseIfPossible)
A (sub-)region of the voxels.
|
BoundedVoxels<T> |
BoundedVoxels.regionIntersecting(BoundingBox box,
int voxelValueForRest)
Like
BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean) but only expects a bounding-box that intersects at least partially. |
BoundedVoxels<T> |
BoundedVoxels.regionZ(int zMin,
int zMax,
VoxelsFactoryTypeBound<T> factory)
Creates an box with a subrange of the slices.
|
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<?> |
BinaryVoxelsFactory.createEmptyOff(Extent extent,
VoxelDataType dataType)
Creates an empty binary-voxels of a particular data-type with all voxels initialized to
off.
|
Modifier and Type | Method and Description |
---|---|
static BufferedImage |
BufferedImageFromVoxels.createGrayscaleByte(Voxels<UnsignedByteBuffer> voxels)
Creates a
BufferedImage from a Voxels<UnsignedByteBuffer> . |
static BufferedImage |
BufferedImageFromVoxels.createGrayscaleShort(Voxels<UnsignedShortBuffer> voxels)
Creates a
BufferedImage from a Voxels<UnsignedShortBuffer> . |
Modifier and Type | Method and Description |
---|---|
static VoxelDataType |
CombineTypes.combineTypes(VoxelDataType type1,
VoxelDataType type2)
What data-type to use to represent voxels of both
type1 and type2 ? |
Modifier and Type | Method and Description |
---|---|
static <V> GraphWithPayload<V,Integer> |
NeighborGraph.create(List<V> vertices,
java.util.function.Function<V,ObjectMask> vertexToObject,
Extent sceneExtent,
boolean preventObjectIntersection,
boolean do3D)
Like
NeighborGraph.create(ObjectCollection, Extent, boolean, boolean) but extracts objects from a
list of elements which form the vertices. |
static GraphWithPayload<ObjectMask,Integer> |
NeighborGraph.create(ObjectCollection objects,
Extent sceneExtent,
boolean preventObjectIntersection,
boolean do3D)
Create the graph with object-masks as vertices, where edges represent the number of
neighboring voxels between objects.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectMask.region(BoundingBox box,
boolean reuseIfPossible)
A (sub-)region of the object-mask.
|
ObjectMask |
ObjectMask.regionIntersecting(BoundingBox box)
Creates an object-mask covering the a bounding-box (that is required to intersect at least
partially)
|
ObjectMask |
ObjectMask.regionZ(int zMin,
int zMax)
Creates an object-mask with a subrange of the slices.
|
Modifier and Type | Method and Description |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
MorphologicalDilation.dilate(BinaryVoxels<UnsignedByteBuffer> voxels,
int iterations,
DilationContext context)
Performs a morphological dilation operation.
|
static ObjectMask |
MorphologicalDilation.dilate(ObjectMask object,
Optional<Extent> extent,
boolean useZ,
int iterations,
boolean bigNeighborhood)
Dilates an
ObjectMask , growing the bounding-box as necessary. |
static BinaryVoxels<UnsignedByteBuffer> |
MorphologicalErosion.erode(BinaryVoxels<UnsignedByteBuffer> voxels,
int iterations,
boolean useZ,
Optional<java.util.function.Predicate<Point3i>> precondition)
Performs a morphological erosion on a
BinaryVoxels<UnsignedByteBuffer> voxels . |
static ObjectMask |
MorphologicalErosion.erode(ObjectMask object,
int iterations,
boolean useZ)
Performs a morphological erosion on an
ObjectMask . |
static ObjectMask |
MorphologicalErosion.erode(ObjectMask object,
int iterations,
boolean useZ,
Optional<AcceptIterationPredicate> postcondition)
Performs a morphological erosion on an
ObjectMask - with a postcondition. |
Modifier and Type | Method and Description |
---|---|
Dimensions |
DimensionsCreator.apply(loci.formats.IFormatReader reader,
ReadOptions readOptions,
int seriesIndex) |
Modifier and Type | Method and Description |
---|---|
static ConvertTo<?> |
ConvertToFactory.create(loci.formats.IFormatReader reader,
VoxelDataType targetDataType,
int effectiveBitsPerPixel) |
Modifier and Type | Method and Description |
---|---|
protected abstract String |
FileNamerIndependent.deriveName(File file,
Optional<Path> inputDirectory,
int index)
Derives a unique name for this file.
|
Modifier and Type | Method and Description |
---|---|
abstract VoxelStatistics |
MarkRegion.createStatisticsFor(VoxelizedMarkMemo memo,
Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
abstract EnergyScheme |
EnergySchemeCreator.create() |
EnergyScheme |
EnergySchemeCreatorByElement.create() |
Modifier and Type | Method and Description |
---|---|
Dictionary |
DictionaryForImageCreator.create(EnergyStackWithoutParameters energyStack) |
AddCriteriaEnergyPair |
EnergySchemeWithSharedFeatures.createAddCriteria() |
Dictionary |
EnergyScheme.createDictionary()
returns the associated
Dictionary or an empty set, if no dictionary is associated with the energy-scheme. |
Constructor and Description |
---|
EnergyScheme(FeatureList<FeatureInputSingleMemo> elemInd,
FeatureList<FeatureInputPairMemo> elemPair,
FeatureList<FeatureInputAllMemo> elemAll,
RegionMap regionMap,
AddCriteriaPair pairAddCriteria) |
EnergyScheme(FeatureList<FeatureInputSingleMemo> elemInd,
FeatureList<FeatureInputPairMemo> elemPair,
FeatureList<FeatureInputAllMemo> elemAll,
RegionMap regionMap,
AddCriteriaPair pairAddCriteria,
Optional<DictionaryProvider> dictionary,
List<NamedBean<Feature<FeatureInputStack>>> listImageFeatures) |
Modifier and Type | Method and Description |
---|---|
static MarksInitialization |
MarksInitializationFactory.create(Optional<? extends ExportSharedObjects> input,
InitializationContext context,
Optional<Define> define) |
static MarksInitialization |
MarksInitializationFactory.createFromExisting(InitializationContext context,
Optional<Define> define,
Optional<SharedObjects> sharedObjects,
Optional<Dictionary> dictionary) |
Modifier and Type | Method and Description |
---|---|
static DisplayStack |
BackgroundCreator.createBackground(NamedProviderStore<Stack> stackCollection,
String backgroundStackName,
StackDisplayer displayer) |
Modifier and Type | Method and Description |
---|---|
ObjectWithProperties |
OverlayMark.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
protected ImageInitialization |
DefineOutputter.createInitialization(InitializationContext context,
ExportSharedObjects input) |
protected ImageInitialization |
DefineOutputter.createInitialization(InitializationContext context,
Optional<SharedObjects> sharedObjects,
Optional<Dictionary> dictionary) |
Constructor and Description |
---|
DualStack(EnergyStack energyStack,
StackDisplayer displayer)
Creates to infer a background from the energy-stack.
|
Modifier and Type | Method and Description |
---|---|
abstract ObjectWithProperties |
Overlay.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut)
Derives an object-mask representation of the overlay to be drawn with
overlayWriter . |
Modifier and Type | Method and Description |
---|---|
ObjectWithProperties |
OverlayObjectMask.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
abstract T |
AnnotationComparisonAssigner.createAssignment(ObjectsToCompare objectsToCompare,
Dimensions dimensions,
boolean useMIP,
InputOutputContext context) |
OverlappingObjects |
FeatureCostAssigner.createAssignment(ObjectsToCompare objectsToCompare,
Dimensions dimensions,
boolean useMIP,
InputOutputContext context) |
ObjectVoxelIntersection |
MaskIntersectionAssigner.createAssignment(ObjectsToCompare objectsToCompare,
Dimensions dimensions,
boolean useMIP,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
AutoLocalThreshold.createFromSource(Channel channel) |
Modifier and Type | Method and Description |
---|---|
ChannelConverter<UnsignedByteBuffer> |
ScaleByDictionary.createConverter() |
Modifier and Type | Method and Description |
---|---|
protected abstract Mask |
FromChannelBase.createFromSource(Channel source) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
FromChannel.createFromSource(Channel source) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
SegmentChannel.createFromSource(Channel source) |
protected Mask |
Threshold.createFromSource(Channel source) |
Modifier and Type | Method and Description |
---|---|
protected ColoredObjectCollection |
ThreeColoredObjects.coloredObjectsToDraw(Dimensions backgroundDimensions) |
protected abstract ColoredObjectCollection |
ColoredBase.coloredObjectsToDraw(Dimensions backgroundDimensions)
Creates colored-objects to be drawn.
|
protected ColoredObjectCollection |
ColoredMask.coloredObjectsToDraw(Dimensions backgroundDimensions) |
protected ColoredObjectCollection |
ColoredBaseWithGenerator.coloredObjectsToDraw(Dimensions backgroundDimensions) |
protected ObjectCollection |
ColoredObjects.objectsToDraw(Dimensions backgroundDimensions) |
protected abstract ObjectCollection |
ColoredBaseWithGenerator.objectsToDraw(Dimensions backgroundDimensions)
The objects to draw (without any colors) on the background
|
Modifier and Type | Method and Description |
---|---|
abstract DisplayStack |
ThumbnailFromStack.thumbnailFor(Stack stack)
Creates a thumbnail for a stack
|
DisplayStack |
ScaleToSize.thumbnailFor(Stack stack) |
Modifier and Type | Method and Description |
---|---|
static LevelResultCollection |
LevelResultCollectionFactory.createCollection(Channel channel,
ObjectCollection objects,
CalculateLevel calculateLevel,
int numDilations,
MessageLogger logger) |
Modifier and Type | Method and Description |
---|---|
protected CheckedFunction<Channel,Channel,CreateException> |
AggregateChannelTask.createChannelDeriver(ChannelSource source) |
Modifier and Type | Method and Description |
---|---|
FeatureExporter<FeatureList<S>> |
SingleRowPerInput.createExporter(LabelHeaders metadataHeaders,
List<NamedBean<FeatureListProvider<S>>> features,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context) |
abstract FeatureExporter<S> |
FeatureSource.createExporter(LabelHeaders metadataHeaders,
List<NamedBean<FeatureListProvider<U>>> features,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context)
Creates the
FeatureExporter to be used for calculating and exporting feature-results. |
Modifier and Type | Method and Description |
---|---|
protected abstract CheckedFunction<Channel,S,CreateException> |
GroupedStackBase.createChannelDeriver(ChannelSource source)
A function to derive the individual type used for aggregation from a
Channel . |
Modifier and Type | Method and Description |
---|---|
protected CheckedFunction<Channel,Histogram,CreateException> |
ExportImageHistograms.createChannelDeriver(ChannelSource source) |
Modifier and Type | Method and Description |
---|---|
static <T extends FeatureInput> |
FeatureExporter.create(FeatureOutputNames outputNames,
FeatureTableCalculator<T> features,
LabelHeaders identifierHeaders,
Optional<InputGrouper> grouper,
FeatureExporterContext context)
Alternative static constructor that creates a shared-state from a
NamedFeatureStore . |
static <T extends FeatureInput> |
FeatureExporter.create(List<NamedBean<FeatureListProvider<T>>> features,
LabelHeaders metadataHeaders,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context)
Alternative static constructor that creates a shared-state from a list of named
FeatureListProvider s. |
static <T extends FeatureInput> |
FeatureExporter.create(NamedFeatureStore<T> featureStore,
LabelHeaders metadataHeaders,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context)
Alternative static constructor that creates a shared-state from a
NamedFeatureStore . |
Constructor and Description |
---|
SharedStateFilteredImageOutput(Outputter baseOutputter,
ImageLabeller<T> filter,
String outputNameMapping,
String outputNameImages) |
Constructor and Description |
---|
SharedStateSegmentInstance(ConcurrentModelPool<T> modelPool,
FeatureTableCalculator<FeatureInputSingleObject> featureTable,
LabelHeaders identifierHeaders,
String outputNameFeatures,
FeatureExporterContext context) |
Constructor and Description |
---|
SharedStateSelectedSlice(Outputter baseOutputter) |
Modifier and Type | Method and Description |
---|---|
DisplayStack |
ThumbnailBatch.thumbnailFor(T element)
Creates a thumbnail for an element in the batch
|
Modifier and Type | Method and Description |
---|---|
ChannelMap |
Autoname.create(OpenedImageFile openedFile,
Logger logger) |
ChannelMap |
FromMetadata.create(OpenedImageFile openedFile,
Logger logger) |
ChannelMap |
SingleChannel.create(OpenedImageFile openedFile,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
void |
CopyFilesMethod.makeCopy(Path source,
Path destination)
Makes a copy of the file at
source at destination . |
void |
CompressAnyTIFF.makeCopyWithDirectory(Path source,
Path destination) |
void |
Bytewise.makeCopyWithDirectory(Path source,
Path destination) |
protected abstract void |
CopyFilesMethod.makeCopyWithDirectory(Path source,
Path destination)
Like
CopyFilesMethod.makeCopy(Path,Path) but after any necessary directories are created so destination can be written. |
Modifier and Type | Method and Description |
---|---|
protected String |
NormalizedPath.deriveName(File file,
Optional<Path> inputDirectory,
int index) |
protected String |
RelativeToDirectory.deriveName(File file,
Optional<Path> inputDirectory,
int index) |
Modifier and Type | Method and Description |
---|---|
protected ObjectCollection |
ColoredMarks.objectsToDraw(Dimensions backgroundDimensions) |
Modifier and Type | Method and Description |
---|---|
FeatureExporter<FeatureTableCalculator<T>> |
FromObjects.createExporter(LabelHeaders metadataHeaders,
List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>> features,
FeatureOutputNames outputNames,
Optional<InputGrouper> grouper,
FeatureExporterContext context) |
Constructor and Description |
---|
IndexedCSVRows(ReadByLine csvFile,
ColumnDefinition columnDefinition)
Creates an index of the rows of the CSV file according to a particular columnDefinition
|
Modifier and Type | Method and Description |
---|---|
static VoxelizedMarksWithEnergy |
VoxelizedMarksWithEnergyFactory.createFromMarks(MarkCollection marks,
KernelCalculationContext context,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
static org.opencv.core.Mat |
ConvertToMat.fromObject(ObjectMask object)
Convert a
ObjectMask to a Mat . |
static org.opencv.core.Mat |
ConvertToMat.fromStack(Stack stack)
Converts a
Stack to a Mat . |
static org.opencv.core.Mat |
ConvertToMat.makeRGBStack(Stack stack,
boolean swapRedBlueChannels)
Derives a
Mat representing an RGB stack. |
Constructor and Description |
---|
EllipseStandardFormConverter(cern.colt.matrix.DoubleMatrix1D matrix) |
Modifier and Type | Method and Description |
---|---|
static Ellipsoid |
EllipsoidFactory.createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>,CreateException> opPoints,
Dimensions dimensions,
boolean suppressZCovariance,
double shell) |
Modifier and Type | Method and Description |
---|---|
static Ellipsoid |
EllipsoidFactory.createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>,CreateException> opPoints,
Dimensions dimensions,
boolean suppressZCovariance,
double shell) |
static Ellipsoid |
EllipsoidFactory.createMarkEllipsoidLeastSquares(ObjectMask object,
Dimensions dimensions,
boolean suppressZCovariance,
double shell)
Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an
object-mask
|
Modifier and Type | Method and Description |
---|---|
static List<Point2i> |
ConvexHullUtilities.pointsOnOutline(ObjectMask object) |
Modifier and Type | Method and Description |
---|---|
static <T extends FeatureInput> |
FeaturesFromXmlFixture.createFeatureList(String xmlPath,
TestLoader loader) |
static <T extends FeatureInput> |
FeaturesFromXmlFixture.createNamedFeatureProviders(String xmlPath,
TestLoader loader) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.