Modifier and Type | Method and Description |
---|---|
OverlappingObjects |
AssignOverlappingObjects.createAssignment(ObjectCollection left,
ObjectCollection right,
double maxAcceptedCost,
Dimensions dimensions)
Creates an assignment from the objects in
left to those in right . |
Modifier and Type | Method and Description |
---|---|
abstract Findable<ObjectCollection> |
ComparableSource.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context)
Loads the source of elements from the file-system and converts to a
ObjectCollection . |
Modifier and Type | Method and Description |
---|---|
default ObjectCollection |
AnnotationWithMarks.convertToObjects(Dimensions dimensions)
Creates an object-collection that is a voxelized representation of the marks in the
annotation.
|
Modifier and Type | Method and Description |
---|---|
Dimensions |
EnergyStackWithoutParameters.dimensions()
The dimensions of all channels in the stack.
|
Dimensions |
EnergyStack.dimensions()
The image-dimensions associated with the energy-stack.
|
Constructor and Description |
---|
EnergyStack(Dimensions dimensions)
Create a new stack of
Dimensions with zero-voxel values, without any additional
parameters. |
EnergyStackWithoutParameters(Dimensions dimensions)
Create a energy-stack with no channels - but with associated dimensions.
|
Modifier and Type | Method and Description |
---|---|
abstract Dimensions |
FeatureInputDimensions.dimensions()
The dimensions of the associated image.
|
Dimensions |
FeatureInputEnergy.dimensions() |
Dimensions |
FeatureInputEnergy.dimensionsRequired()
The image-dimensions associated with the energy-stack, or an exception if no energy-stack
exists.
|
Modifier and Type | Method and Description |
---|---|
Optional<Dimensions> |
FeatureInputEnergy.dimensionsOptional()
The image-dimensions associated with the energy-stack, if it exists.
|
Modifier and Type | Method and Description |
---|---|
protected Dimensions |
ChannelAggregator.maybeDropResolution(Dimensions dimensions)
Removes the
Resolution component in Dimensions . |
Modifier and Type | Method and Description |
---|---|
protected abstract Optional<Dimensions> |
ChannelAggregator.existingDimensions()
The
Dimensions to use for the aggregation. |
Modifier and Type | Method and Description |
---|---|
protected Dimensions |
ChannelAggregator.maybeDropResolution(Dimensions dimensions)
Removes the
Resolution component in Dimensions . |
Modifier and Type | Method and Description |
---|---|
abstract ObjectCollection |
ObjectFilter.filter(ObjectCollection objectsToFilter,
Optional<Dimensions> dimensions)
Filters an
ObjectCollection to remove objects. |
Modifier and Type | Method and Description |
---|---|
abstract ScaleFactor |
ScaleCalculator.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize)
Calculates a scaling-factor for a source image/entity of particular dimensions.
|
Modifier and Type | Method and Description |
---|---|
Dimensions |
Channel.dimensions()
The size and voxel-resolution of the channel.
|
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFactory.create(Dimensions dimensions,
VoxelDataType channelDataType)
Creates an empty initialized channel for a particular data-type.
|
Channel |
ChannelFactorySingleType.createEmptyInitialised(Dimensions dimensions)
Create a
Channel initialized with zero-valued voxel-buffers. |
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.
|
Channel |
ChannelFactorySingleType.createEmptyUninitialised(Dimensions dimensions)
Create a
Channel without initialization with voxel-buffers. |
Channel |
ChannelFactory.createUninitialised(Dimensions dimensions,
VoxelDataType channelDataType)
Create a
Channel without initialization with voxel-buffers. |
Modifier and Type | Method and Description |
---|---|
Dimensions |
OrientationChange.dimensions(Dimensions dimensions)
A
Dimensions that describes {code dimensions} after the orientation change. |
Dimensions |
Dimensions.duplicateChangeExtent(Extent extentToAssign)
Deep-copies the current object, but assigns a different
Extent . |
Dimensions |
Dimensions.duplicateChangeResolution(Optional<Resolution> resolutionToAssign)
Deep-copies the current object, but assigns a different
Resolution . |
Dimensions |
Dimensions.duplicateChangeZ(int z)
Deep-copies the current object, but assigns a different size for the Z-dimension.
|
Dimensions |
Dimensions.resizeXY(int x,
int y)
Resizes the dimensions to have new sizes in the X and Y dimension.
|
Dimensions |
Dimensions.scaleXYBy(ScaleFactor scaleFactor)
Scales the X- and Y- dimensions by a scaling-factor.
|
Modifier and Type | Method and Description |
---|---|
Dimensions |
OrientationChange.dimensions(Dimensions dimensions)
A
Dimensions that describes {code dimensions} after the orientation change. |
boolean |
Dimensions.equals(Dimensions other,
boolean compareResolution)
Checks equality between this object and another
Dimensions , but possibly skipping a
comparison of image-resolution in the check. |
Modifier and Type | Method and Description |
---|---|
Dimensions |
Mask.dimensions()
The size and voxel-resolution of the channel.
|
Modifier and Type | Method and Description |
---|---|
static Mask |
MaskFromObjects.createFromNotObjects(ObjectCollection objects,
Dimensions dimensions,
BinaryValuesInt outValues)
Create a
Mask corresponding to all off voxels in an ObjectCollection . |
static Mask |
MaskFromObjects.createFromObjects(ObjectCollection objects,
Dimensions dimensions,
BinaryValuesInt outValues)
Create a
Mask corresponding to all on voxels in an ObjectCollection . |
static Mask |
MaskFactory.createMaskOff(Dimensions dimensions)
Creates a binary-mask for specific dimensions with all voxels set to off.
|
static Mask |
MaskFactory.createMaskOff(Dimensions dimensions,
BinaryValuesInt binaryValues)
Creates a binary-mask for specific dimensions with all voxels set to off.
|
static Mask |
MaskFactory.createMaskOn(Dimensions dimensions)
Creates a binary-mask for specific dimensions with all voxels set to on.
|
static Mask |
MaskFactory.createMaskOn(Dimensions dimensions,
BinaryValuesInt binaryValues)
Creates a binary-mask for specific dimensions with all voxels set to on.
|
Constructor and Description |
---|
Mask(Dimensions dimensions,
BinaryValuesInt binaryValues)
Creates a new empty mask of particular dimensions and with particular
BinaryValuesInt . |
Modifier and Type | Method and Description |
---|---|
Dimensions |
RGBStack.dimensions()
The dimensions of all channels in the stack.
|
Dimensions |
DisplayStack.dimensions()
The dimensions of all channels in the stack.
|
Dimensions |
Stack.dimensions()
The dimensions of all channels in the stack.
|
Dimensions |
ImageMetadata.getDimensions()
The dimensions of the image.
|
Constructor and Description |
---|
ImageMetadata(Dimensions dimensions,
int numberChannels,
int numberFrames,
int numberSeries,
boolean rgb,
int bitDepthPerChannel,
ImageFileAttributes fileAttributes,
Optional<java.time.ZonedDateTime> acquisitionTime,
Optional<ImagePyramidMetadata> pyramid) |
RGBStack(Dimensions dimensions,
ChannelFactorySingleType factory)
Creates a particularly-sized stack with all channels initialized to 0.
|
Stack(Dimensions dimensions,
ChannelFactorySingleType factory,
int numberChannels,
boolean rgb)
Create with a particular number of empty
Channel s. |
Modifier and Type | Method and Description |
---|---|
NamedStacks |
NamedStacks.applyOperation(java.util.function.UnaryOperator<Stack> operation,
Optional<Dimensions> dimensions)
Applies an operation on each
Stack in the collection and returns a new derived
collection. |
Modifier and Type | Method and Description |
---|---|
Dimensions |
FeatureInputImageMetadata.dimensions() |
Modifier and Type | Method and Description |
---|---|
DualScale<Dimensions> |
ImageInferenceContext.getDimensions()
The size of the image for which we wish to segment, before and after any scaling for model
inference.
|
Constructor and Description |
---|
ImageInferenceContext(DualScale<Dimensions> dimensions,
ScaleFactor scaleFactor,
Optional<List<String>> classLabels,
VoxelsResizer resizer,
ExecutionTimeRecorder executionTimeRecorder,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
abstract Dimensions |
NamedChannelsInput.dimensions(int seriesIndex,
Logger logger)
Dimensions of a particular series.
|
Modifier and Type | Method and Description |
---|---|
Dimensions |
OpenedNamedChannels.dimensions(Logger logger) |
Dimensions |
NamedChannelsConcatenate.dimensions(Logger logger) |
Dimensions |
NamedChannelsMap.dimensions(Logger logger)
The dimensions of each
Channel . |
Modifier and Type | Method and Description |
---|---|
Dimensions |
ObjectsAsGrayscaleGenerator.dimensions()
The dimensions associated with the objects (assumed to be constant across any change in
element).
|
Constructor and Description |
---|
ObjectsAsGrayscaleGenerator(Dimensions dimensions) |
ObjectsAsUniqueValueGenerator(Dimensions dimensions)
Create with a particular dimensions.
|
ObjectsMergedAsMaskGenerator(Dimensions dimensions)
Create with particular size for the mask image.
|
Modifier and Type | Method and Description |
---|---|
io.vavr.control.Either<Dimensions,DisplayStack> |
ObjectsAsRGBGenerator.getBackground()
A background image or dimensions to define an empty background.
|
Modifier and Type | Method and Description |
---|---|
protected static RGBStack |
ObjectsAsRGBGenerator.createEmptyStackFor(Dimensions dimensions)
Creates an empty
RGBStack . |
Modifier and Type | Method and Description |
---|---|
protected RGBStack |
DrawObjectsGenerator.generateBackgroundRegion(ObjectCollectionWithProperties objects,
io.vavr.control.Either<Dimensions,DisplayStack> background) |
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. |
static DrawObjectsGenerator |
DrawObjectsGenerator.outlineVariedColors(int numberColors,
int outlineWidth,
io.vavr.control.Either<Dimensions,DisplayStack> background)
Creates a generator that draws an outline around objects on a background using varied colors
for the objects.
|
void |
ObjectsAsRGBGenerator.setBackground(io.vavr.control.Either<Dimensions,DisplayStack> background)
A background image or dimensions to define an empty background.
|
Constructor and Description |
---|
ObjectsAsRGBGenerator(DrawObject drawObject,
ObjectDrawAttributes attributes,
io.vavr.control.Either<Dimensions,DisplayStack> background) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
OpenedImageFile.dimensionsForSeries(int seriesIndex,
Logger logger)
The
Dimensions associated with a particular series. |
Modifier and Type | Method and Description |
---|---|
Dimensions |
DimensionsCreator.apply(loci.formats.IFormatReader reader,
ReadOptions readOptions,
int seriesIndex) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
ImageFileShape.getImageDimensions() |
Modifier and Type | Method and Description |
---|---|
void |
ConvertTo.copyAllChannels(Dimensions dimensions,
ByteBuffer source,
DestinationChannelForIndex destination,
int z,
ImageFileEncoding sourceImageEncoding,
OrientationChange orientationCorrection)
Copies the channels in the source buffer into a particular
DestinationChannelForIndex . |
protected void |
ConvertTo.setupBefore(Dimensions dimensions,
ImageFileEncoding sourceImageEncoding)
Always called before any batch of calls to
ConvertTo.convertSliceOfSingleChannel(java.nio.ByteBuffer, int, org.anchoranalysis.image.core.dimensions.OrientationChange) . |
Constructor and Description |
---|
ImageFileShape(Dimensions imageDimensions,
int numberChannels,
int numberFrames) |
Modifier and Type | Method and Description |
---|---|
protected void |
FloatFromUnsignedByte.setupBefore(Dimensions dimensions,
ImageFileEncoding encoding) |
Modifier and Type | Method and Description |
---|---|
abstract VoxelStatistics |
MarkRegion.createStatisticsFor(VoxelizedMarkMemo memo,
Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
Optional<Mark> |
CreateMarkFromPoints.fitMarkToPointsFromMarks(MarkCollection marks,
Dimensions dimensions)
Extract points from a marks, creates a new mark from markProvider and then fits this mark the
extracted points
|
Modifier and Type | Method and Description |
---|---|
abstract void |
PointsFitter.fit(List<Point3f> points,
Mark mark,
Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
abstract Optional<Orientation> |
OrientationProposer.propose(Mark mark,
Dimensions dimensions,
RandomNumberGenerator randomNumberGenerator) |
abstract Optional<List<Point3i>> |
PointsProposer.propose(Point3d point,
Mark mark,
Dimensions dimensions,
RandomNumberGenerator randomNumberGenerator,
ErrorNode errorNode) |
abstract Optional<Point3d> |
RadiiProposer.propose(Point3d pos,
RandomNumberGenerator randomNumberGenerator,
Dimensions dimensions,
Orientation orientation) |
Modifier and Type | Method and Description |
---|---|
boolean |
AddCriteriaOr.includeMarks(VoxelizedMarkMemo mark1,
VoxelizedMarkMemo mark2,
Dimensions dimensions,
Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session,
boolean do3D) |
boolean |
ArbitraryPointCommon.includeMarks(VoxelizedMarkMemo mark1,
VoxelizedMarkMemo mark2,
Dimensions dimensions,
Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session,
boolean do3D) |
abstract boolean |
AddCriteriaPair.includeMarks(VoxelizedMarkMemo mark1,
VoxelizedMarkMemo mark2,
Dimensions dimensions,
Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session,
boolean do3D) |
boolean |
BoundingBoxIntersection.includeMarks(VoxelizedMarkMemo mark1,
VoxelizedMarkMemo mark2,
Dimensions dimensions,
Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
FeatureInputMark.getDimensionsRequired() |
Modifier and Type | Method and Description |
---|---|
Optional<Dimensions> |
FeatureInputMark.getDimensionsOptional() |
Modifier and Type | Method and Description |
---|---|
abstract double |
PxlListOperationFromMark.doOperation(VoxelizedMarkMemo pxlMarkMemo,
Dimensions dimensions) |
Constructor and Description |
---|
FeatureInputMark(Mark mark,
Dimensions dimensions,
Dictionary dictionary) |
Constructor and Description |
---|
FeatureInputMark(Mark mark,
Optional<Dimensions> dimensions) |
FeatureInputMark(Mark mark,
Optional<Dimensions> dimensions,
Optional<Dictionary> dictionary) |
Modifier and Type | Method and Description |
---|---|
Optional<Dimensions> |
FeatureInputMarkCollection.dimensions() |
Constructor and Description |
---|
FeatureInputMarkCollection(MarkCollection marks,
Optional<Dimensions> dimensions) |
Modifier and Type | Method and Description |
---|---|
protected Dimensions |
ReportFeatureForMarks.createImageDim() |
Constructor and Description |
---|
MarksAsUniqueValueGenerator(Dimensions dimensions,
RegionMembershipWithFlags regionMembership) |
Modifier and Type | Method and Description |
---|---|
abstract BoundingBox |
Mark.box(Dimensions dimensions,
int regionID) |
abstract BoundingBox |
Mark.boxAllRegions(Dimensions dimensions) |
List<BoundingBox> |
MarkCollection.boxList(Dimensions dimensions,
int regionID) |
static Point3d |
PointClamper.clamp(Point3d point,
Dimensions dimensions) |
static Point3i |
PointClamper.clamp(Point3i point,
Dimensions dimensions) |
ObjectMask |
Mark.deriveObject(Dimensions dimensions,
RegionMembershipWithFlags region,
BinaryValuesByte binaryValues)
Create a
ObjectMask representation of the Mark . |
ObjectCollection |
MarkCollection.deriveObjects(Dimensions dimensions,
RegionMembershipWithFlags regionMembership) |
ColoredMarks |
ColoredMarks.subsetWhereBBoxIntersects(Dimensions dimensions,
int regionID,
List<BoundingBox> intersectList) |
Constructor and Description |
---|
MarkToObjectConverter(Dimensions dimensions)
Create for particular
Dimensions without a scaling-factor. |
MarkToObjectConverter(Optional<ScaleFactor> scaleFactor,
Dimensions dimensions)
Create for particular
Dimensions with a scaling-factor. |
MarkToObjectConverter(Optional<ScaleFactor> scaleFactor,
Dimensions dimensions,
RegionMembershipWithFlags regionMembership,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
BoundingBox |
MarkWithPositionAndSingleRadius.box(Dimensions dimensions,
int regionID) |
BoundingBox |
Ellipsoid.box(Dimensions dimensions,
int regionID) |
BoundingBox |
Ellipse.box(Dimensions dimensions,
int regionID) |
BoundingBox |
MarkWithPositionAndSingleRadius.boxAllRegions(Dimensions dimensions) |
BoundingBox |
Ellipsoid.boxAllRegions(Dimensions dimensions) |
BoundingBox |
Ellipse.boxAllRegions(Dimensions dimensions) |
static BoundingBox |
BoundingBoxCalculator.boxFromBounds(Point3d pos,
double radius,
boolean do3D,
Dimensions dimensions)
Calculates a bounding box for a point with a scalar radius in all dimensions.
|
static BoundingBox |
BoundingBoxCalculator.boxFromBounds(Point3d center,
cern.colt.matrix.DoubleMatrix1D radiiMatrix,
boolean do3D,
Dimensions dimensions)
Calculates a bounding box for a point with varying radii in each dimension (that have already
been resolved into a matrix)
|
Modifier and Type | Method and Description |
---|---|
BoundingBox |
RotatableBoundingBox.box(Dimensions dimensions,
int regionID) |
BoundingBox |
PointListBase.box(Dimensions dimensions,
int regionID) |
BoundingBox |
LineSegment.box(Dimensions dimensions,
int regionID) |
BoundingBox |
PointList.boxAllRegions(Dimensions dimensions) |
BoundingBox |
RotatableBoundingBox.boxAllRegions(Dimensions dimensions) |
BoundingBox |
PolygonCurve.boxAllRegions(Dimensions dimensions) |
BoundingBox |
Polygon.boxAllRegions(Dimensions dimensions) |
BoundingBox |
LineSegment.boxAllRegions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
BoundingBox |
OverlayMark.box(DrawOverlay overlayWriter,
Dimensions dim) |
ObjectWithProperties |
OverlayMark.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
ProposerContext.dimensions() |
Modifier and Type | Method and Description |
---|---|
abstract double |
Kernel.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntens,
Dimensions dimensions,
double densityRatio) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
TransformationContext.dimensions() |
Constructor and Description |
---|
TransformationContext(Dimensions dimensions,
KernelCalculationContext kernelCalcContext,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
abstract BoundingBox |
Overlay.box(DrawOverlay overlayWriter,
Dimensions dimensions)
A bounding-box around the overlay.
|
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 |
---|---|
ColoredOverlayCollection |
ColoredOverlayCollection.subsetWhereBoxIntersects(Dimensions scene,
DrawOverlay drawOverlay,
List<BoundingBox> toIntersectWith)
Find overlays whose bounding-boxes intersect with any of the boxes in
toIntersectWith . |
Modifier and Type | Method and Description |
---|---|
BoundingBox |
OverlayObjectMask.box(DrawOverlay overlayWriter,
Dimensions dimensions) |
ObjectWithProperties |
OverlayObjectMask.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
Findable<ObjectCollection> |
Objects.loadAsObjects(Path filePathSource,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
DualMarksAnnotationAsObjects.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
MarksAsObjects.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
Findable<ObjectCollection> |
MaskAsObject.loadAsObjects(Path reference,
Dimensions dimensions,
boolean debugMode,
OperationContext context) |
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 Channel |
DistanceTransformForEachObject3D.createFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
abstract void |
BlurStrategy.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
void |
BlurGaussian3D.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
void |
BlurGaussianEachSlice2D.blur(VoxelsUntyped voxels,
Dimensions dimensions,
MessageLogger logger) |
protected double |
BlurStrategy.calculateSigma(Dimensions dimensions,
MessageLogger logger) |
Modifier and Type | Method and Description |
---|---|
protected Optional<Dimensions> |
ProjectableBufferAggregator.existingDimensions() |
Modifier and Type | Method and Description |
---|---|
protected abstract Channel |
FromDimensionsBase.createFromDimensions(Dimensions dimensions) |
protected Channel |
CreateNew.createFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
protected Channel |
RepeatSlice.createFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
SpecifyDimensions.get() |
Dimensions |
FromChannel.get() |
Dimensions |
GuessDimensions.get() |
Modifier and Type | Method and Description |
---|---|
protected Mask |
AllValuesOff.createFromDimensions(Dimensions dimensions) |
protected abstract Mask |
FromDimensionsBase.createFromDimensions(Dimensions dimensions) |
protected Mask |
AllValuesOn.createFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
FromObjects.createFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
Box.createFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
ObjectCollection |
ObjectFilterPredicate.filter(ObjectCollection objectsToFilter,
Optional<Dimensions> dimensions) |
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) |
protected void |
ObjectFilterPredicate.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
ObjectFilterRelation.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
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) |
protected void |
DiscardOutliers.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
RelationWithMatches.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
Modifier and Type | Method and Description |
---|---|
ObjectCollection |
And.filter(ObjectCollection objects,
Optional<Dimensions> dim) |
ObjectCollection |
Or.filter(ObjectCollection objectsToFilter,
Optional<Dimensions> dim) |
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) |
protected void |
ThresholdedVolume.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
ThresholdedFeature.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
GreaterIntersectionWith.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
IntersectsWith.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
protected void |
IntensityGreaterEqualThan.start(Optional<Dimensions> dimensions,
ObjectCollection objectsToFilter) |
Modifier and Type | Method and Description |
---|---|
protected Dimensions |
WithDimensionsBase.createDimensions() |
Modifier and Type | Method and Description |
---|---|
protected Optional<Dimensions> |
WithOptionalDimensionsBase.createDims()
Returns the dimensions or null if none are provided
|
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 |
---|---|
ScaleFactor |
FitTo.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
ToDimensions.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
ConstantScaleFactor.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
ToSuggested.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
Invert.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
ScaleFactor |
MinimumXYResolution.calculate(Optional<Dimensions> dimensionsToBeScaled,
Optional<ImageSizeSuggestion> suggestedSize) |
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 |
---|---|
static void |
DimensionsChecker.check(Channel channelToCheck,
String channelToCheckName,
Dimensions dimFromChannel)
Checks a channel to make sure it's the same size as an an existing channel.
|
static void |
DimensionsChecker.check(Mask maskToCheck,
String channelToCheckName,
Dimensions dimensionsFromChannel)
Checks a channel to make sure it's the same size as an an existing channel
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Modifier and Type | Method and Description |
---|---|
protected double |
Extent.calculateForAxis(Dimensions dimensions,
Axis axis) |
protected abstract double |
ForSpecificAxis.calculateForAxis(Dimensions dimensions,
Axis axis) |
protected double |
VoxelPhysicalSize.calculateForAxis(Dimensions dimensions,
Axis axis) |
protected double |
Area.calculateFromDimensions(Dimensions dim) |
protected double |
Volume.calculateFromDimensions(Dimensions dim) |
protected double |
ForSpecificAxis.calculateFromDimensions(Dimensions dim) |
protected abstract double |
FromDimensionsBase.calculateFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
static ObjectCollection |
ObjectIntersectionRemover.removeIntersectingVoxels(ObjectCollection objects,
Dimensions dimensions,
boolean errorDisconnectedObjects) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
OpenedMultiFile.dimensionsForSeries(int seriesIndex,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
boolean |
AddCriteriaFeatureRelationThreshold.includeMarks(VoxelizedMarkMemo mark1,
VoxelizedMarkMemo mark2,
Dimensions dimensions,
Optional<FeatureCalculatorMulti<FeatureInputPairMemo>> session,
boolean do3D) |
Modifier and Type | Method and Description |
---|---|
Optional<Orientation> |
RandomOrientation.propose(Mark mark,
Dimensions dimensions,
RandomNumberGenerator randomNumberGenerator) |
Optional<Orientation> |
RandomXY.propose(Mark mark,
Dimensions dimensions,
RandomNumberGenerator randomNumberGenerator) |
Modifier and Type | Method and Description |
---|---|
Optional<List<Point3i>> |
IncludeRandomObjects.propose(Point3d point,
Mark mark,
Dimensions dimensions,
RandomNumberGenerator randomNumberGenerator,
ErrorNode errorNode) |
Optional<List<Point3i>> |
XYOrientationExtendToZ.propose(Point3d point,
Mark mark,
Dimensions dimensions,
RandomNumberGenerator randomNumberGenerator,
ErrorNode errorNode) |
Modifier and Type | Method and Description |
---|---|
Optional<Point3d> |
RadiiProposerRepeat.propose(Point3d pos,
RandomNumberGenerator randomNumberGenerator,
Dimensions dimensions,
Orientation orientation) |
Optional<Point3d> |
UniformRandomRadiiProposer.propose(Point3d pos,
RandomNumberGenerator randomNumberGenerator,
Dimensions dimensions,
Orientation orientation) |
Modifier and Type | Method and Description |
---|---|
protected ObjectCollection |
ColoredMarks.objectsToDraw(Dimensions backgroundDimensions) |
Modifier and Type | Method and Description |
---|---|
double |
KernelBirthAndKill.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelBirth.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelSplit.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelMerge.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelInitialMarksFromPartition.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelExchange.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelDeath.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelInitialMarksVoxelized.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelInitialMarksProposed.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntensity,
Dimensions dimensions,
double densityRatio) |
double |
KernelReplace.calculateAcceptanceProbability(int existingSize,
int proposalSize,
double poissonIntens,
Dimensions dimensions,
double densityRatio) |
Modifier and Type | Method and Description |
---|---|
Dimensions |
PointsFitterToMark.createDim() |
Modifier and Type | Method and Description |
---|---|
protected abstract void |
LinearLeastSquaresViaNormalEquationBase.applyCoefficientsToMark(cern.colt.matrix.DoubleMatrix2D matrixV,
Mark mark,
Dimensions dimensions) |
void |
FitResult.applyFitResultToMark(Ellipsoid mark,
Dimensions sceneDim,
double shell) |
void |
Reference.fit(List<Point3f> points,
Mark mark,
Dimensions dimensions) |
void |
ReflectInAxesWithinDistance.fit(List<Point3f> points,
Mark mark,
Dimensions dimensions) |
void |
LinearLeastSquaresEllipseFitter.fit(List<Point3f> points,
Mark mark,
Dimensions dimensions) |
void |
LinearLeastSquaresEllipsoidFitter.fit(List<Point3f> points,
Mark mark,
Dimensions dimensions) |
void |
LinearLeastSquaresViaNormalEquationBase.fit(List<Point3f> points,
Mark mark,
Dimensions dimensions) |
void |
PointsFitterToMark.fitPointsToMark(List<Point3f> pointsForFitter,
Mark mark,
Dimensions dim) |
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
|
Constructor and Description |
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CutOffCornersObjectFixture(Dimensions dimensions)
Create with any check on dimensions.
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Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.