Modifier and Type | Method and Description |
---|---|
CostMatrix<ObjectMask> |
AssignOverlappingObjects.getCosts()
A matrix linking the overlap between each
ObjectMask to each other, respectively as
rows and columns. |
List<ObjectMask> |
OverlappingObjects.getLeftUnassigned()
The unassigned objects in the left set.
|
List<ObjectMask> |
OverlappingObjects.getRightUnassigned()
The unassigned objects in the right set.
|
List<ObjectMask> |
ObjectVoxelIntersection.paired(boolean left) |
List<ObjectMask> |
OverlappingObjects.paired(boolean left) |
List<ObjectMask> |
ObjectVoxelIntersection.unassigned(boolean left) |
List<ObjectMask> |
OverlappingObjects.unassigned(boolean left) |
Modifier and Type | Method and Description |
---|---|
void |
OverlappingObjects.addAssignedPair(ObjectMask object1,
ObjectMask object2,
double overlapRatio)
Adds an assigned pair of objects with a particular overlap-ratio.
|
void |
OverlappingObjects.addUnassignedLeft(ObjectMask object)
Add an unassigned object to the left set.
|
void |
OverlappingObjects.addUnassignedRight(ObjectMask object)
Add an unassigned object to the right set.
|
Constructor and Description |
---|
ObjectVoxelIntersection(ObjectMask left,
ObjectMask right)
Determines a voxel-assignment between two objects.
|
Modifier and Type | Method and Description |
---|---|
Stack |
DrawColoredObjects.createObjectsImage(Assignment<ObjectMask> assignment,
boolean left,
AssignmentColorPool colorPool)
Creates an image with the objects colored, as indicated in the class description.
|
Stack |
AssignmentGenerator.transform(Assignment<ObjectMask> element) |
Modifier and Type | Method and Description |
---|---|
protected static void |
SegmentChannelIntoObjects.checkUnsupportedObjectMask(Optional<ObjectMask> objectMask)
Throws an exception if
object is present, as it is unsupported by the implementation. |
ObjectCollection |
SegmentChannelIntoObjectsUnary.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds) |
abstract ObjectCollection |
SegmentChannelIntoObjects.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds)
Segments a channel to produce an object-collection.
|
protected abstract ObjectCollection |
SegmentChannelIntoObjectsUnary.segment(Channel channel,
Optional<ObjectMask> object,
Optional<ObjectCollection> seeds,
SegmentChannelIntoObjects upstreamSegmenter)
Creates an
ObjectCollection given the segmentation-results provided by the delegate. |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderGlobal.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
abstract BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask)
Thresholds voxels (across a range of values) so that they have only binary range (i.e.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
Channel.equalMask(BoundingBox box,
int equalValue)
|
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
FindContour.createFrom(ObjectMask object,
int numberErosions,
boolean do3D,
boolean atImageBoundary)
Creates an contour from a
ObjectMask . |
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
FindContour.createFrom(ObjectMask object,
int numberErosions,
boolean do3D,
boolean atImageBoundary)
Creates an contour from a
ObjectMask . |
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
MaskInverter.invertObjectDuplicate(ObjectMask object)
Creates a new object-mask where off voxels become on voxels and vice versa.
|
ObjectMask |
Mask.region(BoundingBox box,
boolean reuseIfPossible)
Creates an
ObjectMask corresponding to the on/off state in a bounding-box. |
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
MaskInverter.invertObjectDuplicate(ObjectMask object)
Creates a new object-mask where off voxels become on voxels and vice versa.
|
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
ObjectMaskMerger.merge(ObjectCollection objects)
Merges all the objects together that are found in a collection.
|
static ObjectMask |
ObjectMaskMerger.merge(ObjectMask first,
ObjectMask second)
Merges two objects together.
|
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
ObjectMaskMerger.merge(ObjectMask first,
ObjectMask second)
Merges two objects together.
|
Modifier and Type | Method and Description |
---|---|
static BoundingBox |
ObjectMaskMerger.mergeBoundingBoxes(java.util.stream.Stream<ObjectMask> objects)
Merges all the bounding boxes of a stream of objects.
|
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
ObjectFromPointsFactory.create(Collection<Point3i> points)
Create an
ObjectMask from a collection of points. |
ObjectMask |
MatchedObject.getSource()
The source object (which is matched against others)
|
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramFromObjectsFactory.createFrom(Channel channel,
ObjectMask object)
|
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramFromObjectsFactory.createFrom(VoxelsUntyped voxels,
Optional<ObjectMask> object)
|
Constructor and Description |
---|
MatchedObject(ObjectMask source,
ObjectCollection matches) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
OverlappingObject.getAfterPreoperation()
After pre-operation but before scaling
|
Modifier and Type | Method and Description |
---|---|
T |
DecodeLabels.CreateElementFromScaledObject.createFrom(int index,
ObjectMask scaledObject)
Create from an index and it's scaled-object.
|
Constructor and Description |
---|
OverlappingObject(T original,
ObjectMask afterPreoperation) |
Constructor and Description |
---|
LabelObjects(java.util.function.Function<T,ObjectMask> extractObject,
java.util.function.BiFunction<T,ReadableTuple3i,T> shiftElement) |
LabelObjects(Optional<java.util.function.UnaryOperator<T>> operationBeforeLabelling,
Optional<java.util.function.Consumer<OverlappingObject<T>>> overlappingObjectConsumer,
java.util.function.Function<T,ObjectMask> extractObject,
java.util.function.BiFunction<T,ReadableTuple3i,T> shiftElement) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectWithProperties.asObjectMask()
Exposes the underlying
ObjectMask ignoring any properties. |
Modifier and Type | Method and Description |
---|---|
void |
ObjectCollectionWithProperties.add(ObjectMask object)
Add an
ObjectMask to the collection, assigning empty properties to it. |
Modifier and Type | Method and Description |
---|---|
ObjectWithProperties |
ObjectWithProperties.map(java.util.function.UnaryOperator<ObjectMask> operator)
Maps the underlying object-mask to another object-mask, reusing the same properties object.
|
Constructor and Description |
---|
ObjectCollectionWithProperties(ObjectMask object)
Create with a single object.
|
ObjectWithProperties(ObjectMask object)
Creates with an existing
ObjectMask and empty properties. |
ObjectWithProperties(ObjectMask object,
Map<String,Object> properties) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
AccessObjectMaskSimple.clipTo(ObjectMask element,
Extent extent) |
ObjectMask |
AccessObjectMaskSimple.createFrom(int index,
ObjectMask object) |
ObjectMask |
AccessObjectMaskSimple.objectFor(ObjectMask element) |
ObjectMask |
AccessObjectMask.objectFor(T element)
An object-mask for a given element.
|
ObjectMask |
AccessObjectMaskSimple.shiftBy(ObjectMask element,
ReadableTuple3i quantity) |
Modifier and Type | Method and Description |
---|---|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor)
Scales every object-mask in a collection collectively.
|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor,
boolean overlappingObjects,
Extent clipTo)
Scales every object-mask in a collection collectively, ensuring the results remain
inside a particular region.
|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor,
boolean overlappingObjects,
Optional<java.util.function.UnaryOperator<ObjectMask>> preOperation,
Optional<java.util.function.UnaryOperator<ObjectMask>> postOperation)
Scales every object-mask in a collection collectively (if not overlappjng), allowing
for additional manipulation before and after scaling.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
AccessObjectMaskSimple.clipTo(ObjectMask element,
Extent extent) |
T |
AccessObjectMask.createFrom(int index,
ObjectMask object)
Creates an element of type
T from an object-representation and index. |
ObjectMask |
AccessObjectMaskSimple.createFrom(int index,
ObjectMask object) |
ObjectMask |
AccessObjectMaskSimple.objectFor(ObjectMask element) |
ObjectMask |
AccessObjectMaskSimple.shiftBy(ObjectMask element,
ReadableTuple3i quantity) |
Modifier and Type | Method and Description |
---|---|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor,
boolean overlappingObjects,
Optional<java.util.function.UnaryOperator<ObjectMask>> preOperation,
Optional<java.util.function.UnaryOperator<ObjectMask>> postOperation)
Scales every object-mask in a collection collectively (if not overlappjng), allowing
for additional manipulation before and after scaling.
|
static ScaledElements<ObjectMask> |
Scaler.scaleObjects(ObjectCollection objects,
ScaleFactor factor,
boolean overlappingObjects,
Optional<java.util.function.UnaryOperator<ObjectMask>> preOperation,
Optional<java.util.function.UnaryOperator<ObjectMask>> postOperation)
Scales every object-mask in a collection collectively (if not overlappjng), allowing
for additional manipulation before and after scaling.
|
Modifier and Type | Method and Description |
---|---|
static List<Point2i> |
PointsFromObject.listFrom2i(ObjectMask object)
A list of two-dimensional integer points from the entire object-mask.
|
static List<Point3d> |
PointsFromObject.listFrom3d(ObjectMask object)
A list of points from the entire object-mask as
Point3d . |
static List<Point3i> |
PointsFromObject.listFrom3i(ObjectMask object)
A list of three-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
|
static List<Point3i> |
PointsFromObject.listFromOutline3i(ObjectMask object)
A list of points as
Point3i from the outline of an object-mask. |
static SortedSet<Point3i> |
PointsFromObject.setFrom3i(ObjectMask object)
A sorted-set of three-dimensional integer points from the entire object-mask
|
static Set<Point3i> |
PointsFromObject.setFromContour(ObjectMask object)
A set of points from the contour of
object in three dimensions. |
Modifier and Type | Method and Description |
---|---|
Optional<ObjectMask> |
RGBStack.objectWithColor(RGBColor color)
Extracts an
ObjectMask from a Channel of all voxels that have a particular
color. |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
FeatureInputPairObjects.getFirst() |
ObjectMask |
FeatureInputPairObjects.getMerged()
Returns a merged version of the two-objects available (or null if not available)
|
ObjectMask |
FeatureInputSingleObject.getObject() |
ObjectMask |
FeatureInputPairObjects.getSecond() |
Modifier and Type | Method and Description |
---|---|
Optional<ObjectMask> |
FeatureInputPairObjects.getMergedOptional() |
Constructor and Description |
---|
FeatureInputPairObjects(ObjectMask first,
ObjectMask second) |
FeatureInputPairObjects(ObjectMask first,
ObjectMask second,
EnergyStack energyStack) |
FeatureInputPairObjects(ObjectMask first,
ObjectMask second,
Optional<EnergyStack> energyStack) |
FeatureInputPairObjects(ObjectMask first,
ObjectMask second,
Optional<EnergyStack> energyStack,
Optional<ObjectMask> merged) |
FeatureInputSingleObject(ObjectMask object) |
FeatureInputSingleObject(ObjectMask object,
EnergyStack energyStack) |
FeatureInputSingleObject(ObjectMask object,
Optional<EnergyStack> energyStack) |
Constructor and Description |
---|
FeatureInputPairObjects(ObjectMask first,
ObjectMask second,
Optional<EnergyStack> energyStack,
Optional<ObjectMask> merged) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectForReduction.getElement()
The underlying
ObjectMask with whom a confidence and label is associated. |
Modifier and Type | Method and Description |
---|---|
LabelledWithConfidence<ObjectMask> |
ObjectForReduction.getLabelled()
The underlying labelled
ObjectMask for input to a reduction algorithm. |
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ReduceElementsGreedy.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
protected abstract boolean |
ReduceElementsGreedy.shouldObjectsBeProcessed(ObjectMask source,
ObjectMask other)
Whether to include another (possibly-overlapping with
source ) element in processing? |
protected boolean |
RemoveOverlappingObjects.shouldObjectsBeProcessed(ObjectMask source,
ObjectMask other) |
Modifier and Type | Method and Description |
---|---|
static List<ObjectForReduction> |
ObjectForReductionFactory.populateFromList(List<LabelledWithConfidence<ObjectMask>> list)
Creates a list of
ObjectForReduction s from a corresponding list of labelled ObjectMask s. |
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ReduceElementsGreedy.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
Constructor and Description |
---|
ObjectForReduction(LabelledWithConfidence<ObjectMask> labelled)
Creates with a
ObjectMask that is considered newly-added. |
ObjectForReduction(LabelledWithConfidence<ObjectMask> labelled,
int index) |
ReduceObjectsGraph(List<LabelledWithConfidence<ObjectMask>> elements)
Create with a list of elements.
|
Modifier and Type | Method and Description |
---|---|
ReduceElements<ObjectMask> |
SuppressNonMaximum.getReduce()
The algorithm for reducing the number of object-masks.
|
Modifier and Type | Method and Description |
---|---|
void |
SuppressNonMaximum.setReduce(ReduceElements<ObjectMask> reduce)
The algorithm for reducing the number of object-masks.
|
Constructor and Description |
---|
SuppressNonMaximum(SegmentStackIntoObjectsPooled<T> segment,
ReduceElements<ObjectMask> reduce,
boolean separateEachLabel) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
MultiScaleObject.getInputScale()
Gets the
ObjectMask at the scale associated with the input-image. |
ObjectMask |
MultiScaleObject.getModelScale()
Gets the
ObjectMask at the scale associated with the segmentation. |
Modifier and Type | Method and Description |
---|---|
List<LabelledWithConfidence<ObjectMask>> |
SegmentedObjectsAtScale.listWithLabels()
Create a
List of all contained objects, including confidence. |
List<WithConfidence<ObjectMask>> |
SegmentedObjectsAtScale.listWithoutLabels()
Create a
List of all contained objects, including confidence. |
Modifier and Type | Method and Description |
---|---|
static <T,S> MultiScaleObject |
MultiScaleObject.extractFrom(DualScale<T> dual1,
DualScale<S> dual2,
java.util.function.BiFunction<T,S,ObjectMask> extractObject)
|
static <T> MultiScaleObject |
MultiScaleObject.extractFrom(DualScale<T> dual,
java.util.function.Function<T,ObjectMask> extractObject)
|
SegmentedObjects |
SegmentedObjects.reduce(ReduceElements<ObjectMask> reduce,
boolean separateEachLabel,
ExecutionTimeRecorder executionTimeRecorder)
Reduces the segmented-objects, applying a reduction algorithm separately to each
object-class.
|
Constructor and Description |
---|
MultiScaleObject(java.util.function.Supplier<ObjectMask> inputScale,
java.util.function.Supplier<ObjectMask> modelScale)
Creates with a separate supplier of an
ObjectMask for each respective scale. |
MultiScaleObject(java.util.function.Supplier<ObjectMask> inputScale,
java.util.function.Supplier<ObjectMask> modelScale)
Creates with a separate supplier of an
ObjectMask for each respective scale. |
SegmentedObjectsAtScale(List<LabelledWithConfidence<MultiScaleObject>> source,
java.util.function.Function<MultiScaleObject,ObjectMask> extractObject,
Stack background,
StackDisplayer displayer,
ExecutionTimeRecorder executionTimeRecorder,
String executionTimeSuffix) |
Modifier and Type | Method and Description |
---|---|
Stack |
ObjectAsMaskGenerator.transform(ObjectMask element) |
Modifier and Type | Method and Description |
---|---|
Stack |
DrawObjectOnStackGenerator.transform(BoundedList<ObjectMask> element) |
Modifier and Type | Method and Description |
---|---|
void |
VoxelsUntyped.copyVoxelsTo(ObjectMask objectSource,
VoxelsUntyped destination,
BoundingBox boxDestination)
Copies the voxels into a
destination , but only those voxels inside an ObjectMask . |
Modifier and Type | Method and Description |
---|---|
void |
VoxelsArithmetic.addTo(ObjectMask object,
int valueToBeAdded)
Adds a constant-value to each voxel but only for voxels inside an object-mask.
|
void |
VoxelsArithmetic.multiplyBy(ObjectMask object,
double factor)
Multiplies each voxel by constant factor but only for voxels inside an
ObjectMask . |
Modifier and Type | Method and Description |
---|---|
void |
VoxelsAssigner.toEitherTwoObjects(ObjectMask object1,
ObjectMask object2,
BoundingBox restrictTo)
Sets voxels to a value if the position is on in either of two masks
|
void |
VoxelsAssigner.toObject(ObjectMask object)
Sets voxels in a box to a particular value if they match an object-mask
|
void |
VoxelsAssigner.toObject(ObjectMask object,
BoundingBox restrictTo)
Sets voxels in a box to a particular value if they match a object-mask (but only a part of
the object-mask)
|
void |
VoxelsAssigner.toObjectIf(ObjectMask object,
java.util.function.IntPredicate voxelPredicate)
Sets voxels in a box to a particular value if they match an object-mask and a voxel
matches a predicate
|
boolean |
VoxelsAssigner.toObjectWhile(ObjectMask object,
java.util.function.IntPredicate voxelPredicate)
Sets voxels in a box to a particular value if they match an object-mask and each voxel
matches a predicate
|
Modifier and Type | Method and Description |
---|---|
void |
VoxelsExtracter.objectCopyTo(ObjectMask from,
Voxels<T> voxelsDestination,
BoundingBox destinationBox)
Copies an area corresponding to an object-mask to another
Voxels . |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
VoxelsPredicate.deriveObject(BoundingBox box)
Creates an
ObjectMask for all the voxels inside the bounding-box satisfying the
predicate. |
ObjectMask |
PredicateImplementation.deriveObject(BoundingBox box) |
ObjectMask |
PredicateAtCorner.deriveObject(BoundingBox box) |
Modifier and Type | Method and Description |
---|---|
Optional<ObjectMask> |
VoxelsPredicate.deriveObjectTight()
Creates an
ObjectMask for all the voxels satisfying the predicate, minimally fitting
the bounding-box to the on voxels only. |
Optional<ObjectMask> |
PredicateImplementation.deriveObjectTight() |
Optional<ObjectMask> |
PredicateAtCorner.deriveObjectTight() |
Modifier and Type | Method and Description |
---|---|
int |
VoxelsPredicate.countForObject(ObjectMask object)
Counts the number of values satisfying the predicate - but restricted to voxels corresponding
to on in an object-mask.
|
int |
PredicateImplementation.countForObject(ObjectMask object) |
int |
PredicateAtCorner.countForObject(ObjectMask object) |
Modifier and Type | Method and Description |
---|---|
static <T> boolean |
IterateVoxelsObjectMask.allMatchIntensity(ObjectMask object,
Voxels<T> voxels,
java.util.function.IntPredicate predicate)
Do all points on an object-mask match a predicate on the point's voxel-intensity?
|
static <T> void |
IterateVoxelsObjectMask.withBuffer(ObjectMask object,
Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel in an object-mask - with one associated buffer for each
slice from
Voxels . |
static void |
IterateVoxelsObjectMask.withPoint(ObjectMask firstMask,
Optional<ObjectMask> secondMask,
ProcessPoint process)
Iterate over each point that is located on an object-mask AND optionally a second-mask
|
static void |
IterateVoxelsObjectMask.withPoint(ObjectMask object,
ProcessPoint process)
Iterate over each voxel that is located on an object-mask
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel with a corresponding on value in an object-mask - and with
two associated buffers for each slice covering the all the global space
i.e.
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoMixedBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinaryMixed<S,T> process)
Iterate over each voxel in an object-mask - with one associated voxel-buffer and
one associated buffer for each slice.
|
static <S,T> void |
IterateVoxelsObjectMask.withTwoVoxelBuffers(ObjectMask object,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessVoxelBufferBinary<S,T> process)
Iterate over each voxel in an object-mask - with two associated voxel-buffers and for
each slice.
|
static <T> void |
IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object,
Voxels<T> voxels,
Optional<BoundingBox> restrictTo,
ProcessVoxelBufferUnary<T> process)
Iterate over each voxel on an object-mask with one associated
VoxelBuffer . |
static <T> void |
IterateVoxelsObjectMask.withVoxelBuffer(ObjectMask object,
Voxels<T> voxels,
ProcessVoxelBufferUnary<T> process)
Iterate over each voxel on an object-mask with one associated
VoxelBuffer . |
Modifier and Type | Method and Description |
---|---|
static <T> void |
IterateVoxelsObjectMaskOptional.withBuffer(Optional<ObjectMask> objectMask,
Voxels<T> voxels,
ProcessBufferUnary<T> process)
Iterate over each voxel (or optionally only on object-mask) with one associated
buffer.
|
static void |
IterateVoxelsObjectMask.withPoint(ObjectMask firstMask,
Optional<ObjectMask> secondMask,
ProcessPoint process)
Iterate over each point that is located on an object-mask AND optionally a second-mask
|
static void |
IterateVoxelsObjectMaskOptional.withPoint(Optional<ObjectMask> objectMask,
Extent extent,
ProcessPoint process)
Iterate over all points that are located on a object-mask or else all points in an extent.
|
static void |
IterateVoxelsObjectMaskOptional.withSlidingBuffer(Optional<ObjectMask> objectMask,
SlidingBuffer<?> buffer,
ProcessPoint process)
Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a
certain object
|
static <S,T> void |
IterateVoxelsObjectMaskOptional.withTwoBuffers(Optional<ObjectMask> objectMask,
Voxels<S> voxels1,
Voxels<T> voxels2,
ProcessBufferBinary<S,T> process)
Iterate over each voxel (or optionally only on object-mask) with two associated
buffers.
|
Modifier and Type | Method and Description |
---|---|
static int |
CountVoxelsIntersectingObjects.countIntersectingVoxels(ObjectMask object1,
ObjectMask object2)
Counts the number of intersecting-voxels between two object-masks.
|
static boolean |
CountVoxelsIntersectingObjects.hasIntersectingVoxels(ObjectMask object1,
ObjectMask object2)
Determines whether there are any intersecting voxels on two object-masks.
|
Modifier and Type | Method and Description |
---|---|
static <T> ProcessVoxelNeighbor<T> |
ProcessVoxelNeighborFactory.withinMask(ObjectMask object,
ProcessChangedPointAbsoluteMasked<T> process)
Creates to process neighbors that must lie within an
ObjectMask . |
static <T> ProcessVoxelNeighbor<T> |
ProcessVoxelNeighborFactory.withinMask(ObjectMask object,
ProcessVoxelNeighborAbsolute<T> process)
Creates to process neighbors that must lie within an
ObjectMask . |
Modifier and Type | Method and Description |
---|---|
static <T> ProcessVoxelNeighbor<T> |
ProcessVoxelNeighborFactory.within(Optional<ObjectMask> containingMask,
Extent extentFallback,
ProcessVoxelNeighborAbsolute<T> process)
Creates to process neighbors that must lie within either an object-mask or an extent (as a
fallback).
|
Constructor and Description |
---|
CountKernelNeighborhoodMask(ObjectMask objectRequireHigh)
Create with object-mask.
|
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
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. |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectMask.clampTo(Extent extent)
Makes sure an object fits inside an extent, removing any parts which do not.
|
ObjectMask |
ObjectMask.duplicate()
Creates a deep-copy of the current object-mask.
|
ObjectMask |
ObjectMask.extractSlice(int sliceIndex,
boolean keepIndex)
Extracts one particular slice as an object-mask
|
ObjectMask |
ObjectMask.flattenZ()
A maximum-intensity projection.
|
ObjectMask |
ObjectCollection.get(int index)
Get an
ObjectMask at a particular position in the collection. |
ObjectMask |
ObjectMask.growBuffer(Point3i growthNegative,
Point3i growthPositive,
Optional<Extent> clipRegion)
Grows the object-mask's voxel buffers in the positive and negative directions by a certain
amount.
|
ObjectMask |
ObjectMask.growToZ(int sizeZ)
Grows a single z-sliced
ObjectMask by duplicating the slice across the z-dimension
sizeZ number of times. |
ObjectMask |
ObjectMask.invert()
Produces a new object-mask that uses the same voxel-buffer but switches the off and
on mapping.
|
ObjectMask |
ObjectMask.mapBoundingBoxChangeExtent(BoundingBox boxToAssign)
Applies a function to map the bounding-box to a new-value (whose extent is expected to change
in value).
|
ObjectMask |
ObjectMask.mapBoundingBoxPreserveExtent(java.util.function.UnaryOperator<BoundingBox> mapOperation)
Applies a function to map the bounding-box to a new-value (whose extent should be unchanged
in value).
|
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.
|
ObjectMask |
ObjectMask.relativeMaskTo(BoundingBox box)
Creates a new object-mask with coordinates changed to be relative to another box.
|
ObjectMask |
ObjectMask.replaceVoxels(Voxels<UnsignedByteBuffer> voxelsToAssign)
Replaces the voxels in the object-mask.
|
ObjectMask |
ObjectMask.scale(ScaleFactor factor)
Produces a scaled-version of an object-mask.
|
ObjectMask |
ObjectMask.scale(ScaleFactor factor,
Optional<Extent> clipTo)
Produces a scaled-version of an object-mask.
|
ObjectMask |
ObjectMask.shiftBackBy(ReadableTuple3i shift)
Shifts the object-mask by moving its bounding-box backwards.
|
ObjectMask |
ObjectMask.shiftBy(ReadableTuple3i shift)
Shifts the object-mask by moving its bounding-box forwards.
|
ObjectMask |
ObjectMask.shiftToOrigin()
Creates a new object-mask with identical voxels but with the bounding-box beginning at the
origin (0,0,0).
|
Modifier and Type | Method and Description |
---|---|
List<ObjectMask> |
ObjectCollection.asList()
Exposes the underlying objects as a
ArrayList . |
static IntersectingObjects<ObjectMask> |
IntersectingObjects.create(ObjectCollection objects)
Creates from an
ObjectCollection . |
Optional<ObjectMask> |
DeriveObjectFromPoints.deriveObject()
Derives an
ObjectMask that includes all points that were previously added. |
java.util.stream.Stream<ObjectMask> |
ObjectMaskStream.filterSubsetStream(java.util.function.Predicate<ObjectMask> predicate,
Collection<Integer> indices)
Like
ObjectMaskStream.filterSubset(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>, java.util.Collection<java.lang.Integer>) but returns a stream rather than a ObjectCollection . |
Optional<ObjectMask> |
ObjectMask.intersect(ObjectMask other,
Extent extent)
Intersects this object-mask with another
|
Iterator<ObjectMask> |
ObjectCollection.iterator() |
java.util.stream.Stream<ObjectMask> |
ObjectCollection.streamIndices(Collection<Integer> indices)
Streams only objects at specific indices.
|
java.util.stream.Stream<ObjectMask> |
ObjectCollection.streamStandardJava()
A stream of object-masks as per Java's standard collections interface.
|
Set<ObjectMask> |
ObjectMaskStream.toSet()
Converts to a
HashSet . |
Modifier and Type | Method and Description |
---|---|
int |
ObjectMask.countIntersectingVoxels(ObjectMask other)
Counts the number of intersecting-voxels between two object-masks.
|
boolean |
ObjectMask.equalsDeep(ObjectMask other)
A deep equality check with another
ObjectMask . |
boolean |
ObjectMask.hasIntersectingVoxels(ObjectMask other)
Determines whether there are any intersecting voxels on two object-masks.
|
Optional<ObjectMask> |
ObjectMask.intersect(ObjectMask other,
Extent extent)
Intersects this object-mask with another
|
Set<T> |
IntersectingObjects.intersectsWith(ObjectMask object)
All elements that intersect with a particular object.
|
java.util.stream.Stream<T> |
IntersectingObjects.intersectsWithStream(ObjectMask object)
Like
IntersectingObjects.intersectsWith(ObjectMask) but returns the objects as a Stream rather
than a Set . |
static ObjectCollection |
ObjectCollectionFactory.of(ObjectMask... object)
Creates a new collection with elements from the parameter-list.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ObjectMaskStream.anyMatch(java.util.function.Predicate<ObjectMask> predicate)
Does the predicate evaluate to true on any object in the collection?
|
<E extends Exception> |
ObjectMaskStream.filter(CheckedPredicate<ObjectMask,E> predicate,
Class<? extends Exception> throwableClass)
Filters a
ObjectCollection to include certain items based on a predicate |
ObjectCollection |
ObjectMaskStream.filter(java.util.function.Predicate<ObjectMask> predicate)
Filters a
ObjectCollection to include certain items based on a predicate |
ObjectCollection |
ObjectMaskStream.filterAndMap(java.util.function.Predicate<ObjectMask> predicate,
java.util.function.UnaryOperator<ObjectMask> mapFunction)
Performs a
ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>) . |
ObjectCollection |
ObjectMaskStream.filterAndMap(java.util.function.Predicate<ObjectMask> predicate,
java.util.function.UnaryOperator<ObjectMask> mapFunction)
Performs a
ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) and then a ObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>) . |
static <T,E extends Exception> |
ObjectCollectionFactory.filterAndMapFrom(Collection<T> collection,
java.util.function.Predicate<T> predicate,
Class<? extends E> throwableClass,
CheckedFunction<T,ObjectMask,E> mapFunction)
Creates a new collection by filtering an iterable and then mapping it to
ObjectMask . |
static <T> ObjectCollection |
ObjectCollectionFactory.filterAndMapFrom(Collection<T> collection,
java.util.function.Predicate<T> predicate,
java.util.function.Function<T,ObjectMask> mapFunction)
Creates a new collection by filtering an iterable and then mapping it to
ObjectMask . |
static <T,E extends Exception> |
ObjectCollectionFactory.filterAndMapWithIndexFrom(List<T> list,
java.util.function.Predicate<T> predicate,
Class<? extends E> throwableClass,
CheckedBiFunction<T,Integer,ObjectMask,E> mapFunctionWithIndex)
Creates a new collection by filtering a list and then mapping from it to
ObjectMask . |
ObjectCollection |
ObjectMaskStream.filterExclude(java.util.function.Predicate<ObjectMask> predicate)
Filters a
ObjectCollection to exclude certain items based on a predicate |
ObjectCollection |
ObjectMaskStream.filterSubset(java.util.function.Predicate<ObjectMask> predicate,
Collection<Integer> indices)
Like
ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>) but only operates on certain indices of the collection. |
java.util.stream.Stream<ObjectMask> |
ObjectMaskStream.filterSubsetStream(java.util.function.Predicate<ObjectMask> predicate,
Collection<Integer> indices)
Like
ObjectMaskStream.filterSubset(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>, java.util.Collection<java.lang.Integer>) but returns a stream rather than a ObjectCollection . |
<E extends Exception> |
ObjectMaskStream.flatMap(Class<? extends Exception> throwableClass,
CheckedFunction<ObjectMask,ObjectCollection,E> mapFunction)
Like a typical
flatMap() operation but accepts a mapping function that throws a
checked exception. |
ObjectCollection |
ObjectMaskStream.flatMap(java.util.function.Function<ObjectMask,ObjectCollection> mapFunction)
Creates a new
ObjectCollection after mapping each item to several others. |
static <T,E extends Exception> |
ObjectCollectionFactory.flatMapFromCollection(java.util.stream.Stream<T> stream,
Class<? extends Exception> throwableClass,
CheckedFunction<T,java.util.stream.Stream<? extends ObjectMask>,E> mapFunction)
Creates a new
ObjectCollection by flatMapping an incoming stream to Collection<ObjectMask> and rethrowing any exception during mapping. |
static <T,E extends Exception> |
ObjectCollectionFactory.flatMapFromStream(java.util.stream.Stream<T> stream,
Class<? extends Exception> throwableClass,
CheckedFunction<T,java.util.stream.Stream<ObjectMask>,E> mapFunction)
Creates a new collection by flat-mapping an incoming stream to
ObjectCollection and
rethrowing any exception during mapping. |
static ObjectCollection |
ObjectCollectionFactory.fromRepeated(int repeats,
java.util.function.Supplier<ObjectMask> createObjectMask)
Creates a new collection by repeatedly calling a function to create a single
ObjectMask . |
static ObjectCollection |
ObjectCollectionFactory.fromSet(Set<ObjectMask> set)
Creates a new collection from a set of
ObjectMask . |
<E extends Exception> |
ObjectMaskStream.map(CheckedFunction<ObjectMask,ObjectMask,E> mapFunction)
Creates a new
ObjectCollection after mapping each item to another. |
<E extends Exception> |
ObjectMaskStream.map(CheckedFunction<ObjectMask,ObjectMask,E> mapFunction)
Creates a new
ObjectCollection after mapping each item to another. |
static <T,E extends Exception> |
ObjectCollectionFactory.mapFrom(Iterable<T> iterable,
Class<? extends E> throwableClass,
CheckedFunction<T,ObjectMask,E> mapFunction)
Creates a new collection by mapping an
Iterable to ObjectMask . |
static <T> ObjectCollection |
ObjectCollectionFactory.mapFrom(Iterable<T> iterable,
java.util.function.Function<T,ObjectMask> mapFunction)
Creates a new collection by mapping an
Iterable to ObjectMask . |
static <T,E extends Exception> |
ObjectCollectionFactory.mapFromOptional(Iterable<T> iterable,
Class<? extends Exception> throwableClass,
CheckedFunction<T,Optional<ObjectMask>,E> mapFunction)
|
static <T> ObjectCollection |
ObjectCollectionFactory.mapFromOptional(Iterable<T> iterable,
java.util.function.Function<T,Optional<ObjectMask>> mapFunction)
|
static <T,E extends Exception> |
ObjectCollectionFactory.mapFromOptional(Iterator<T> iterator,
Class<? extends Exception> throwableClass,
CheckedFunction<T,Optional<ObjectMask>,E> mapFunction)
|
static <T> ObjectCollection |
ObjectCollectionFactory.mapFromOptional(Iterator<T> iterator,
java.util.function.Function<T,Optional<ObjectMask>> mapFunction)
|
static <E extends Exception> |
ObjectCollectionFactory.mapFromRange(int startInclusive,
int endExclusive,
Class<? extends Exception> throwableClass,
CheckedIntFunction<ObjectMask,E> mapFunction)
Creates a new collection by mapping integers (from a range) each to a
ObjectMask . |
static ObjectCollection |
ObjectCollectionFactory.mapFromRange(int startInclusive,
int endExclusive,
java.util.function.IntFunction<ObjectMask> mapFunction)
Creates a new collection by mapping integers (from a range) each to a
ObjectMask . |
<T,E extends Exception> |
ObjectMaskStream.mapToList(CheckedFunction<ObjectMask,T,E> mapFunction)
Creates a new
List after mapping each item to another type. |
<T,E extends Exception> |
ObjectMaskStream.mapToListOptional(CheckedFunction<ObjectMask,Optional<T>,E> mapFunction)
Creates a new
List after mapping each item to another (optional) type |
<T,E extends Exception> |
ObjectMaskStream.mapToSortedSet(CheckedFunction<ObjectMask,T,E> mapFunction)
Creates a new
SortedSet after mapping each item to another type. |
OptionalInt |
ObjectMaskStream.maxAsInt(java.util.function.ToIntFunction<ObjectMask> function)
Finds the maximum value of a function applied to each object in the collection.
|
OptionalInt |
ObjectMaskStream.minAsInt(java.util.function.ToIntFunction<ObjectMask> function)
Finds the minimum value of a function applied to each object in the collection.
|
Constructor and Description |
---|
IntersectingObjects(Collection<T> elements,
java.util.function.Function<T,ObjectMask> extractObject)
Creates an r-tree for particular objects, as extracted from elements.
|
ObjectCollection(ArrayList<ObjectMask> objects)
Creates with the underlying list.
|
ObjectCollection(java.util.stream.Stream<ObjectMask> stream)
Creates with elements from a stream.
|
Modifier and Type | Method and Description |
---|---|
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 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 |
---|---|
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 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 |
---|---|
static BinaryVoxels<UnsignedByteBuffer> |
VoxelsThresholder.threshold(VoxelsUntyped voxels,
float level,
BinaryValuesByte binaryValues,
Optional<ObjectMask> objectMask,
boolean alwaysDuplicate)
Applies thresholding to
VoxelsUntyped . |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
MarkToObjectConverter.convert(Mark mark)
Converts a
Mark to an equivalent ObjectMask . |
ObjectMask |
Mark.deriveObject(Dimensions dimensions,
RegionMembershipWithFlags region,
BinaryValuesByte binaryValues)
Create a
ObjectMask representation of the Mark . |
Constructor and Description |
---|
OverlayObjectMask(ObjectMask object,
int id)
Creates with a particular
ObjectMask and identifier. |
Modifier and Type | Class and Description |
---|---|
class |
CompareAnnotations<T extends Assignment<ObjectMask>>
Task to compare a set of annotations to a segmentation or another set of annotations.
|
class |
ComparisonSharedState<T extends Assignment<ObjectMask>> |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationComparisonAssigner<T extends Assignment<ObjectMask>>
Compares elements in an annotation to elements from an experiment.
|
Modifier and Type | Class and Description |
---|---|
class |
ImageCounterList<T extends Assignment<ObjectMask>>
Allows operations to be applied to several
ImageCounter s collectively. |
Modifier and Type | Method and Description |
---|---|
VoxelsUntyped |
GrayscaleReconstruction2DIJ.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Modifier and Type | Method and Description |
---|---|
protected abstract boolean |
ObjectFilterPredicate.match(ObjectMask object,
Optional<Dimensions> dimensions)
A predicate condition for an object to be kept in the collection
|
protected boolean |
ObjectFilterRelation.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected abstract boolean |
ObjectFilterRelation.match(ObjectMask object,
Optional<Dimensions> dim,
DoubleBiPredicate relation) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
DiscardOutliers.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
RelationWithMatches.match(ObjectMask object,
Optional<Dimensions> dim,
DoubleBiPredicate relation) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
NotTouchingSceneBorder.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
GreaterIntersectionWith.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
IntersectsWith.match(ObjectMask objectToIntersectWith,
Optional<Dimensions> dimensions) |
protected boolean |
IntensityGreaterEqualThan.match(ObjectMask object,
Optional<Dimensions> dimensions) |
protected boolean |
ThresholdedVolume.match(ObjectMask object,
Optional<Dimensions> dim,
DoubleBiPredicate relation) |
protected boolean |
ThresholdedFeature.match(ObjectMask object,
Optional<Dimensions> dim,
DoubleBiPredicate relation) |
Modifier and Type | Method and Description |
---|---|
protected ObjectCollection |
Filter.createFromObjects(ObjectCollection objects,
Optional<List<ObjectMask>> objectsRejected,
Optional<Dimensions> dim) |
protected ObjectCollection |
FilterByGroup.createFromObjects(ObjectCollection objects,
Optional<List<ObjectMask>> objectsRejected,
Optional<Dimensions> dim) |
protected abstract ObjectCollection |
ObjectCollectionProviderFilterBase.createFromObjects(ObjectCollection objects,
Optional<List<ObjectMask>> objectsRejected,
Optional<Dimensions> dim) |
protected ObjectCollection |
ObjectCollectionProviderFilterBase.filter(ObjectCollection objects,
Optional<Dimensions> dim,
Optional<List<ObjectMask>> objectsRejected) |
Modifier and Type | Method and Description |
---|---|
protected ObjectMask |
Dilate.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
protected abstract ObjectMask |
ObjectCollectionProviderMorphological.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
protected ObjectMask |
Erode.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
Modifier and Type | Method and Description |
---|---|
protected ObjectMask |
Dilate.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
protected abstract ObjectMask |
ObjectCollectionProviderMorphological.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
protected ObjectMask |
Erode.applyMorphologicalOperation(ObjectMask object,
Optional<Extent> extent) |
Modifier and Type | Method and Description |
---|---|
abstract Channel |
MinimaImposition.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
Channel |
MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
abstract VoxelsUntyped |
GrayscaleReconstructionByErosion.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
VoxelsUntyped |
GrayscaleReconstructionRobinson.reconstruction(VoxelsUntyped mask,
VoxelsUntyped marker,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
ObjectCollection |
WatershedYeong.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds) |
Modifier and Type | Method and Description |
---|---|
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
ReductionOutcome<LabelledWithConfidence<ObjectMask>> |
ThresholdConfidence.reduce(List<LabelledWithConfidence<ObjectMask>> elements,
Extent extent,
ExecutionTimeRecorder executionTimeRecorder) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
Sequence.segment(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask) |
BinaryVoxels<UnsignedByteBuffer> |
ThresholdAgainstChannel.segment(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> object) |
BinaryVoxels<UnsignedByteBuffer> |
Repeat.segmentFromExistingSegmentation(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask,
BinarySegmentation segment) |
BinaryVoxels<UnsignedByteBuffer> |
Invert.segmentFromExistingSegmentation(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask,
BinarySegmentation segment) |
Modifier and Type | Method and Description |
---|---|
protected double |
HasTouchingVoxels.calculateWithIntersection(ObjectMask first,
ObjectMask second,
BoundingBox boxIntersect) |
protected abstract double |
TouchingVoxels.calculateWithIntersection(ObjectMask object1,
ObjectMask object2,
BoundingBox boxIntersect) |
protected double |
NumberTouchingVoxels.calculateWithIntersection(ObjectMask object1,
ObjectMask object2,
BoundingBox boxIntersect) |
protected double |
NumberTouchingVoxelFaces.calculateWithIntersection(ObjectMask object1,
ObjectMask object2,
BoundingBox boxIntersect) |
protected CountKernel |
TouchingVoxels.createCountKernelMask(ObjectMask object2Relative) |
Modifier and Type | Method and Description |
---|---|
protected abstract double |
OutlineKernelBase.calculateWithParameters(ObjectMask object,
KernelApplicationParameters parameters,
CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack) |
Modifier and Type | Method and Description |
---|---|
protected double |
NumberVoxelsAtBorder.calculateWithParameters(ObjectMask object,
KernelApplicationParameters parameters,
CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack) |
static int |
NumberVoxelsAtBorder.numberBorderPixels(ObjectMask object,
KernelApplicationParameters parameters) |
Modifier and Type | Method and Description |
---|---|
protected abstract double |
SpecificEnergyChannelBase.calculateWithChannel(ObjectMask object,
Channel channel) |
protected double |
CountEqual.calculateWithChannel(ObjectMask object,
Channel channel) |
protected double |
NumberNeighboringVoxels.calculateWithParameters(ObjectMask object,
KernelApplicationParameters parameters,
CheckedSupplier<EnergyStack,FeatureCalculationException> energyStack) |
Modifier and Type | Method and Description |
---|---|
protected double |
IntensityMeanShellMaxSlice.calculateForShell(ObjectMask object,
Channel channel) |
protected double |
IntensityMeanShell.calculateForShell(ObjectMask object,
Channel channel) |
protected abstract double |
IntensityMeanShellBase.calculateForShell(ObjectMask shell,
Channel channel) |
Modifier and Type | Method and Description |
---|---|
protected CalculationPart<ObjectMask,FeatureInputSingleObject> |
Erode.createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject> session) |
protected CalculationPart<ObjectMask,FeatureInputSingleObject> |
Shell.createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject> session) |
protected abstract CalculationPart<ObjectMask,FeatureInputSingleObject> |
DerivedObject.createCachedCalculationForDerived(CalculationPartResolver<FeatureInputSingleObject> session) |
Modifier and Type | Method and Description |
---|---|
protected abstract ObjectMask |
CalculateIncrementalOperationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
protected ObjectMask |
CalculateObjectMask.execute(FeatureInputSingleObject input) |
protected ObjectMask |
CalculateShellObjectMask.execute(FeatureInputSingleObject input) |
protected ObjectMask |
CalculateIncrementalOperationMap.execute(FeatureInputSingleObject input,
Integer key) |
Modifier and Type | Method and Description |
---|---|
static CalculationPart<ObjectMask,FeatureInputSingleObject> |
CalculateShellObjectMask.of(CalculationPartResolver<FeatureInputSingleObject> resolver,
MorphologicalIterations iterations,
int iterationsErosionSecond,
boolean inverse) |
Modifier and Type | Method and Description |
---|---|
protected abstract ObjectMask |
CalculateIncrementalOperationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
Constructor and Description |
---|
CalculateObjectMask(int iterations,
ResolvedPartMap<ObjectMask,FeatureInputSingleObject,Integer> map) |
CalculateShellObjectMask(ResolvedPart<ObjectMask,FeatureInputSingleObject> calculateDilation,
ResolvedPart<ObjectMask,FeatureInputSingleObject> calculateErosion,
int iterationsErosionSecond,
boolean do3D,
boolean inverse) |
CalculateShellObjectMask(ResolvedPart<ObjectMask,FeatureInputSingleObject> calculateDilation,
ResolvedPart<ObjectMask,FeatureInputSingleObject> calculateErosion,
int iterationsErosionSecond,
boolean do3D,
boolean inverse) |
Modifier and Type | Method and Description |
---|---|
protected ObjectMask |
CalculateErosionMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
protected ObjectMask |
CalculateDilationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
static CalculationPart<ObjectMask,FeatureInputSingleObject> |
CalculateErosion.of(CalculationPartResolver<FeatureInputSingleObject> cache,
int iterations,
boolean do3D) |
static ResolvedPart<ObjectMask,FeatureInputSingleObject> |
CalculateDilation.of(CalculationPartResolver<FeatureInputSingleObject> cache,
int iterations,
boolean do3D) |
static ResolvedPart<ObjectMask,FeatureInputSingleObject> |
CalculateErosion.ofResolved(CalculationPartResolver<FeatureInputSingleObject> cache,
int iterations,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
protected ObjectMask |
CalculateErosionMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
protected ObjectMask |
CalculateDilationMap.applyOperation(ObjectMask object,
Extent extent,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
static double |
IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel,
ObjectMask object) |
static double |
IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel,
ObjectMask object,
boolean excludeZero) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
LevelResult.getObject() |
Constructor and Description |
---|
LevelResult(int level,
ObjectMask object,
Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ColoredObject.getObject()
The object-mask.
|
Constructor and Description |
---|
ColoredObject(ObjectMask object,
RGBColor color) |
ColoredObjectCollection(ObjectMask object,
RGBColor color)
Create with a single object and color.
|
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectVertex.getObject() |
Modifier and Type | Method and Description |
---|---|
double |
PayloadCalculator.calculate(ObjectMask object) |
Constructor and Description |
---|
ObjectVertex(ObjectMask object,
double payload) |
Modifier and Type | Method and Description |
---|---|
boolean |
AndCondition.accept(ObjectMask destination) |
boolean |
WrapAsUpdatable.accept(ObjectMask destination) |
boolean |
UpdatableBeforeCondition.accept(ObjectMask destination) |
boolean |
NeighborhoodCondition.accept(ObjectMask destination) |
boolean |
AfterCondition.accept(ObjectMask source,
ObjectMask destination,
ObjectMask merged) |
boolean |
IncreaseFeatureCondition.accept(ObjectMask source,
ObjectMask destination,
ObjectMask merged) |
boolean |
DistanceCondition.accept(ObjectMask source,
ObjectMask destination,
Optional<UnitConverter> unitConverter) |
boolean |
BeforeCondition.accept(ObjectMask source,
ObjectMask destination,
Optional<UnitConverter> unitConverter) |
void |
AndCondition.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
void |
WrapAsUpdatable.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
void |
UpdatableBeforeCondition.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
void |
NeighborhoodCondition.updateSourceObject(ObjectMask source,
Optional<UnitConverter> unitConverter) |
Modifier and Type | Method and Description |
---|---|
protected abstract PrioritisedVertex |
AssignPriority.assignPriorityToEdge(ObjectVertex source,
ObjectVertex destination,
ObjectMask merge,
ErrorReporter errorReporter) |
PrioritisedVertex |
AssignPriorityFromImprovement.assignPriorityToEdge(ObjectVertex source,
ObjectVertex destination,
ObjectMask merged,
ErrorReporter errorReporter) |
PrioritisedVertex |
AssignPriorityFromPair.assignPriorityToEdge(ObjectVertex source,
ObjectVertex destination,
ObjectMask merged,
ErrorReporter errorReporter) |
Constructor and Description |
---|
PrioritisedVertex(ObjectMask object,
double payload,
double priority,
boolean considerForMerge)
Constructor
|
Constructor and Description |
---|
SliceThresholderMask(boolean clearOutsideMask,
ObjectMask object,
BinaryValuesByte binaryValues) |
Constructor and Description |
---|
Steepest(SlidingBuffer<?> buffer,
WatershedEncoding encoder,
boolean do3D,
boolean bigNeighborhood,
Optional<ObjectMask> objectMask)
Create for a specific buffer.
|
Modifier and Type | Method and Description |
---|---|
ObjectCollection |
FloodFillEachIntensityLevel.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Modifier and Type | Method and Description |
---|---|
abstract boolean |
VisitScheduler.considerVisit(Point3i point,
int distanceAlongContour,
ObjectMask object) |
boolean |
VisitSchedulerMaxDistanceAlongContour.considerVisit(Point3i point,
int distanceAlongContour,
ObjectMask object) |
boolean |
VisitSchedulerUniformSample.considerVisit(Point3i point,
int distanceAlongContour,
ObjectMask object) |
boolean |
VisitSchedulerAnd.considerVisit(Point3i point,
int distanceAlongContour,
ObjectMask object) |
boolean |
VisitSchedulerConvexAboutRoot.considerVisit(Point3i point,
int distanceAlongContour,
ObjectMask object) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
SegmentThresholdAboveMinBound.segment(VoxelsUntyped voxels,
BinarySegmentationParameters parameters,
Optional<ObjectMask> objectMask) |
Constructor and Description |
---|
ContourTraverser(ObjectMask contourToTraverse,
ConsiderVisit visitCondition,
boolean useZ,
boolean bigNeighborhood) |
Modifier and Type | Method and Description |
---|---|
ObjectCollectionWithProperties |
Pairwise.findObjectsMatchingRow(CSVRow csvRow,
IntersectingObjects<ObjectMask> allObjects) |
abstract ObjectCollectionWithProperties |
ColumnDefinition.findObjectsMatchingRow(CSVRow csvRow,
IntersectingObjects<ObjectMask> allObjects) |
ObjectCollectionWithProperties |
Single.findObjectsMatchingRow(CSVRow csvRow,
IntersectingObjects<ObjectMask> allObjects) |
Modifier and Type | Method and Description |
---|---|
ObjectCollectionWithProperties |
CSVRow.findObjectsMatchingRow(IntersectingObjects<ObjectMask> allObjects) |
Modifier and Type | Method and Description |
---|---|
static List<Contour> |
CVFindContours.contoursForObject(ObjectMask object)
Calculates the extreme outer contours from an
ObjectMask as OpenCV defines contours. |
Modifier and Type | Method and Description |
---|---|
static org.opencv.core.Mat |
ConvertToMat.fromObject(ObjectMask object)
Convert a
ObjectMask to a Mat . |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
ObjectWithEllipse.getObject() |
Constructor and Description |
---|
ObjectWithEllipse(ObjectMask object,
Ellipse mark) |
Modifier and Type | Method and Description |
---|---|
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 ObjectMask |
CircleObjectFixture.circleAt(Point2i center,
double radius) |
Modifier and Type | Method and Description |
---|---|
void |
WriteIntoDirectory.writeObject(String outputName,
ObjectMask object) |
Modifier and Type | Method and Description |
---|---|
static ObjectMask |
CircleObjectFixture.circleAt(Point2d center,
int radius)
Creates a single circular mask at a particular center point and radius.
|
ObjectMask |
CutOffCornersObjectFixture.create1()
Create the first object.
|
ObjectMask |
CutOffCornersObjectFixture.create2()
Create the second object.
|
ObjectMask |
CutOffCornersObjectFixture.create3()
Create the third object.
|
ObjectMask |
TestLoaderObjects.openLargestObjectFrom(String suffix) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.