Modifier and Type | Class and Description |
---|---|
class |
ChannelProviderBinary
Implementation of
ChannelProvider that calls two ChannelProvider s that
must provide Channel s of the same dimensions. |
class |
ChannelProviderTernary
Implementation of
ChannelProvider that calls three ChannelProvider s that
must provide Channel s of the same dimensions. |
class |
ChannelProviderUnary
Implementation of
ChannelProvider that calls a single delegate ChannelProvider . |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
ChannelProviderUnary.getChannel()
The delegate
ChannelProvider that is called. |
ChannelProvider |
ChannelProviderBinary.getChannel1()
The first delegate
ChannelProvider that is called. |
ChannelProvider |
ChannelProviderTernary.getChannel1()
The first delegate
ChannelProvider that is called. |
ChannelProvider |
ChannelProviderBinary.getChannel2()
The second delegate
ChannelProvider that is called. |
ChannelProvider |
ChannelProviderTernary.getChannel2()
The second delegate
ChannelProvider that is called. |
ChannelProvider |
ChannelProviderTernary.getChannel3()
The third delegate
ChannelProvider that is called. |
Modifier and Type | Method and Description |
---|---|
void |
ChannelProviderUnary.setChannel(ChannelProvider channel)
The delegate
ChannelProvider that is called. |
void |
ChannelProviderBinary.setChannel1(ChannelProvider channel1)
The first delegate
ChannelProvider that is called. |
void |
ChannelProviderTernary.setChannel1(ChannelProvider channel1)
The first delegate
ChannelProvider that is called. |
void |
ChannelProviderBinary.setChannel2(ChannelProvider channel2)
The second delegate
ChannelProvider that is called. |
void |
ChannelProviderTernary.setChannel2(ChannelProvider channel2)
The second delegate
ChannelProvider that is called. |
void |
ChannelProviderTernary.setChannel3(ChannelProvider channel3)
The third delegate
ChannelProvider that is called. |
Modifier and Type | Class and Description |
---|---|
class |
AnisotropicDiffusion
Performs Perona-Malik Anisotropic
Diffusion.
|
class |
MinimumFilter |
Modifier and Type | Class and Description |
---|---|
class |
DistanceTransform3D
Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
|
class |
DistanceTransformForEachObject3D
Like
DistanceTransform3D but applies the distance transform separately for each object in
a collection. |
Modifier and Type | Class and Description |
---|---|
class |
CreateNew
Creates a new channel with all values initialized to a constant (by default zero)
|
class |
Duplicate |
class |
FromDimensionsBase |
class |
FromInput
Finds the input-stack using a conventional name of
input_image - and extracts the first
channel |
class |
FromStack
Extracts a channel from a provider of a stack
|
class |
IfParamEquals |
class |
Reference |
class |
TwoVoxelMappingBase
Takes the two channels and creates a NEW third channel whose pixels are a function of the two
channels
|
class |
UnaryWithObjectsBase |
class |
UnaryWithValueBase
A
ChannelProviderUnary which has a scalar value field |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
IfParamEquals.getChannelElse() |
Modifier and Type | Method and Description |
---|---|
void |
IfParamEquals.setChannelElse(ChannelProvider channelElse) |
Modifier and Type | Class and Description |
---|---|
class |
AddConstant |
class |
ArithmeticWithConstantBase
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a
constant.
|
class |
ArithmeticWithConstantConditionallyWriteBase |
class |
Invert
Subtracts each voxel from the maximum value for the channel's data type (e.g.
|
class |
MaxTwoChannels |
class |
MaxWithConstant |
class |
MeanThreeChannels
Creates a new channel that is the mean of three input channels
|
class |
MinTwoChannels |
class |
MinWithConstant |
class |
MultiplyConstant |
class |
MultiplyTwoChannels |
class |
SubtractFromConstant |
class |
SubtractMean
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
|
class |
SubtractTwoChannels |
Modifier and Type | Class and Description |
---|---|
class |
AssignFromChannel
Copies the pixels from
channelAssignFrom to channel (possibly masking) |
class |
AssignFromDictionary |
class |
AssignFromIntersectingObjects
Matches source-objects to target objects, based upon intersection, and assigns the value in the
respective source object to the target object
|
class |
AssignValue
Assigns a constant (scalar) value to the portion of the image covered by a mask
|
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
AssignFromChannel.getChannelAssignFrom() |
Modifier and Type | Method and Description |
---|---|
void |
AssignFromChannel.setChannelAssignFrom(ChannelProvider channelAssignFrom) |
Modifier and Type | Class and Description |
---|---|
class |
Convert<T>
Converts a channel by applying a converter (no histogram is involved in the conversion).
|
class |
ConvertBase |
class |
ConvertWithHistogram<T>
Converts a channel to a different voxel data-type by applying a converter with an associated
histogram.
|
Modifier and Type | Class and Description |
---|---|
class |
GradientBase
Base class to calculate the gradient of the voxels in a
Channel . |
class |
GradientBaseAddSum
Like
GradientBase but allows an arbitrary constant to be added to voxels storing the
gradient. |
class |
GradientForAxis
Extracts the gradient in the direction of a particular axis (identified by an index)
|
class |
GradientXY
Calculates a
Channel 's gradient along the x and y axes. |
class |
Sobel
3x3 Sobel Filter
|
Modifier and Type | Class and Description |
---|---|
class |
Blur
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
|
class |
IfVoxelZero
Creates a new channel which is a merged version of two input channels according to rules.
|
class |
Median
Applies a median-filter with square kernel
|
class |
NormalizeDifferenceToMedian
Corrects a channel in the following way
|
class |
NormalizeObjectIntensity
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
|
class |
QuantileStretch
Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel
data range
|
class |
ScaleXY
Scales the channel in the X and Y dimensions.
|
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
IfVoxelZero.getChannelIfVoxelZero()
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
|
ChannelProvider |
NormalizeDifferenceToMedian.getChannelLookup() |
Modifier and Type | Method and Description |
---|---|
void |
IfVoxelZero.setChannelIfVoxelZero(ChannelProvider channelIfVoxelZero)
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in
this channel instead
|
void |
NormalizeDifferenceToMedian.setChannelLookup(ChannelProvider channelLookup) |
Modifier and Type | Class and Description |
---|---|
class |
FromMask |
class |
FromMaskBase
A base class for a
ChannelProvider which also uses a binary-mask, but which doesn't use
any other ChannelProvider as an input. |
class |
UnaryWithMaskBase |
class |
ZeroOutsideMask
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
|
Modifier and Type | Class and Description |
---|---|
class |
LevelPerObjectBase
Creates a channel with a level calculated for each object variously
|
class |
LevelPerObjectIndependently
Creates a channel with different threshold-levels for each object, calculating the level only
from the histogram of the particular object.
|
class |
LevelPerObjectNeighbors
Calculates a threshold-level for each object collectively based on other objects
|
Modifier and Type | Class and Description |
---|---|
class |
IdentifyObjects
Assigns a unique id number to each object.
|
class |
ScoreObjects |
class |
ScoreVoxels
Assigns a score (a value indicating how probable something is) to each voxel
|
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
ScoreVoxels.getGradient() |
ChannelProvider |
ScoreVoxels.getIntensity() |
Modifier and Type | Method and Description |
---|---|
List<ChannelProvider> |
ScoreVoxels.getChannelsExtra() |
List<ChannelProvider> |
ScoreObjects.getListAdditionalChannelProviders() |
Modifier and Type | Method and Description |
---|---|
void |
ScoreVoxels.setGradient(ChannelProvider gradient) |
void |
ScoreVoxels.setIntensity(ChannelProvider intensity) |
Modifier and Type | Method and Description |
---|---|
void |
ScoreVoxels.setChannelsExtra(List<ChannelProvider> channelsExtra) |
void |
ScoreObjects.setListAdditionalChannelProviders(List<ChannelProvider> listAdditionalChannelProviders) |
Modifier and Type | Class and Description |
---|---|
class |
ExtractCenterSlice
Extracts the slice at the center (rounding down) of the range of z-stacks.
|
class |
ExtractSliceRange
Extracts slices from
sliceStart (inclusive) to sliceEnd (inclusive). |
class |
MaximumIntensityProjection |
class |
MeanIntensityProjection |
class |
RepeatSlice
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an
existing channel
|
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
RepeatSlice.getSlice() |
Modifier and Type | Method and Description |
---|---|
void |
RepeatSlice.setSlice(ChannelProvider slice) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
FromChannel.getChannel()
The
ChannelProvider to use for dimensions. |
Modifier and Type | Method and Description |
---|---|
void |
FromChannel.setChannel(ChannelProvider channel)
The
ChannelProvider to use for dimensions. |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
FromChannel.getChannel() |
Modifier and Type | Method and Description |
---|---|
void |
FromChannel.setChannel(ChannelProvider channel) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
FromChannelBase.getChannel() |
Modifier and Type | Method and Description |
---|---|
void |
FromChannelBase.setChannel(ChannelProvider channel) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
MorphologicalOperatorBase.getBackgroundChannelProvider() |
Modifier and Type | Method and Description |
---|---|
void |
MorphologicalOperatorBase.setBackgroundChannelProvider(ChannelProvider backgroundChannelProvider) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
IntensityGreaterEqualThan.getChannel() |
Modifier and Type | Method and Description |
---|---|
void |
IntensityGreaterEqualThan.setChannel(ChannelProvider channel) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
UnaryWithChannelBase.getChannel() |
ChannelProvider |
WithChannelBase.getChannel() |
Modifier and Type | Method and Description |
---|---|
void |
UnaryWithChannelBase.setChannel(ChannelProvider channel) |
void |
WithChannelBase.setChannel(ChannelProvider channel) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
ThresholdAgainstChannel.getChannelThreshold() |
Modifier and Type | Method and Description |
---|---|
void |
ThresholdAgainstChannel.setChannelThreshold(ChannelProvider channelThreshold) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
FromChannelOrMask.getChannel()
A channel that is provided to the stack.
|
Modifier and Type | Method and Description |
---|---|
void |
FromChannelOrMask.setChannel(ChannelProvider channel)
A channel that is provided to the stack.
|
Constructor and Description |
---|
FromChannelOrMask(ChannelProvider channel) |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
ThreeChannels.getBlue() |
ChannelProvider |
ThreeChannels.getGreen() |
ChannelProvider |
ThreeChannels.getRed() |
Modifier and Type | Method and Description |
---|---|
void |
ThreeChannels.setBlue(ChannelProvider blue) |
void |
ThreeChannels.setGreen(ChannelProvider green) |
void |
ThreeChannels.setRed(ChannelProvider red) |
Modifier and Type | Method and Description |
---|---|
static Channel |
DimensionsChecker.createSameSize(ChannelProvider provider,
String providerName,
Channel channelSameSize)
Creates a new channel from a provider, making sure it's the same size as an an existing
channel.
|
Modifier and Type | Class and Description |
---|---|
class |
BackgroundSubtractor |
class |
WithFilterBase |
class |
WithRadiusBase
A
ChannelProviderUnary with a 'radius' parameter |
Modifier and Type | Class and Description |
---|---|
class |
EdgeFilterIJ |
class |
GaussianBlur2D |
Modifier and Type | Class and Description |
---|---|
class |
MeanFilter2D |
class |
VarianceFilter2D |
Modifier and Type | Class and Description |
---|---|
class |
MedianFilter2D |
class |
MedianFilter3D |
Modifier and Type | Method and Description |
---|---|
ChannelProvider |
MergeSpatialClusters.getDistanceMapProvider()
A distance map which can also be used for making decisions on merging
|
Modifier and Type | Method and Description |
---|---|
void |
MergeSpatialClusters.setDistanceMapProvider(ChannelProvider distanceMapProvider)
A distance map which can also be used for making decisions on merging
|
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.