Package | Description |
---|---|
org.anchoranalysis.image.bean.threshold |
Base classes for thresholding and calculating levels for thresholding.
|
org.anchoranalysis.image.core.mask |
An image with only two permissible states.
|
org.anchoranalysis.image.core.mask.combine |
Binary operations involving voxelwise combination of
Mask . |
org.anchoranalysis.image.voxel.binary.values |
Defining on and off intensity-values to interpret an image in a binary way.
|
org.anchoranalysis.image.voxel.kernel |
Applying a kernel via
convolution to voxels.
|
org.anchoranalysis.image.voxel.object |
The fundamental data class that is an
ObjectMask
and related structures. |
org.anchoranalysis.image.voxel.thresholder |
Thresholding operations on voxels.
|
org.anchoranalysis.mpp.mark |
Non-bean classes related to
Mark s. |
org.anchoranalysis.mpp.overlay | |
org.anchoranalysis.overlay |
Overlay s and related classes involving drawing entities on top
of an image. |
org.anchoranalysis.overlay.object |
An implementation of an
Overlay that draws an ObjectMask on an image. |
org.anchoranalysis.plugin.fiji.bean.threshold |
Implementations of
Thresholder that use FIJI. |
org.anchoranalysis.plugin.image.segment.thresholder.slice |
Non-beans pertaining to segmenting a z-stack slice-by-slice.
|
org.anchoranalysis.plugin.imagej.bean.threshold |
Implementations of
Thresholder that call ImageJ. |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
Thresholder.threshold(VoxelsUntyped voxels,
BinaryValuesByte binaryValues)
Like
Thresholder.threshold(VoxelsUntyped, BinaryValuesByte, Optional, Optional) applying the
thresholding to the entire set of voxels. |
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 |
---|---|
BinaryValuesByte |
Mask.binaryValuesByte()
The two states which are permitted to be assigned to the voxels, stored as bytes.
|
Modifier and Type | Method and Description |
---|---|
static void |
MaskAnd.apply(Voxels<UnsignedByteBuffer> voxelsFirst,
Voxels<UnsignedByteBuffer> voxelsSecond,
BinaryValuesByte binaryValuesFirst,
BinaryValuesByte binaryValuesSecond)
Performs a logical and operation on each voxel in two
Voxels (considered to be
masks), writing the result onto the second mask. |
Modifier and Type | Method and Description |
---|---|
BinaryValuesByte |
BinaryValuesInt.asByte()
Derives a
BinaryValuesByte representation from the current values. |
static BinaryValuesByte |
BinaryValuesByte.getDefault()
Default values to use, if not otherwise specified.
|
BinaryValuesByte |
BinaryValuesByte.invert()
Inverts the values so off becomes on, and vice-versa.
|
Constructor and Description |
---|
KernelPointCursor(int index,
Point3i point,
Extent extent,
BinaryValuesByte binaryValues,
KernelApplicationParameters parameters)
Creates to be focused around a particular point in the image.
|
Modifier and Type | Method and Description |
---|---|
BinaryValuesByte |
ObjectMask.binaryValuesByte()
What values constitute an on and off state in
voxels - as bytes. |
BinaryValuesByte |
ObjectCollection.getFirstBinaryValuesByte()
The
BinaryValuesByte associated with the first object in the collection. |
Constructor and Description |
---|
ObjectMask(BoundingBox box,
Voxels<UnsignedByteBuffer> voxels,
BinaryValuesByte binaryValues)
Like
ObjectMask(BoundingBox, Voxels, BinaryValuesInt) but specifies the
binary-values as bytes. |
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 . |
static void |
VoxelsThresholder.thresholdByte(Voxels<UnsignedByteBuffer> voxels,
int level,
BinaryValuesByte binaryValues)
Applies thresholding to
Voxels of unsigned byte data type. |
static BinaryVoxels<UnsignedByteBuffer> |
VoxelsThresholder.thresholdFloat(Voxels<FloatBuffer> voxels,
float level,
BinaryValuesByte binaryValues)
Applies thresholding to
Voxels of float data type. |
Modifier and Type | Method and Description |
---|---|
ObjectMask |
Mark.deriveObject(Dimensions dimensions,
RegionMembershipWithFlags region,
BinaryValuesByte binaryValues)
Create a
ObjectMask representation of the Mark . |
Constructor and Description |
---|
MarkToObjectConverter(Optional<ScaleFactor> scaleFactor,
Dimensions dimensions,
RegionMembershipWithFlags regionMembership,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
ObjectWithProperties |
OverlayMark.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
abstract ObjectWithProperties |
Overlay.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut)
Derives an object-mask representation of the overlay to be drawn with
overlayWriter . |
Modifier and Type | Method and Description |
---|---|
ObjectWithProperties |
OverlayObjectMask.createObject(Dimensions dimensionsEntireImage,
BinaryValuesByte binaryValuesOut) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Constructor and Description |
---|
SliceThresholder(BinaryValuesByte binaryValuesByte) |
SliceThresholderMask(boolean clearOutsideMask,
ObjectMask object,
BinaryValuesByte binaryValues) |
SliceThresholderWithoutMask(BinaryValuesByte binaryValues) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.