Uses of Class
org.anchoranalysis.image.bean.provider.ChannelProvider
Packages that use ChannelProvider
Package
Description
Base classes for providers of different core data entities related to images.
Implementations of
ChannelProvider
that use FIJI.Euclidean Distance Transform
implementations via FIJI.
Implementations of
ChannelProvider
that are
generic base-classes or otherwise abstract or general.Implementations of
ChannelProvider
that perform
arithmetic on voxels in one or more Channel
s.Implementations of
ChannelProvider
that sets the
values of the voxels in a Channel
.Implementations of
ChannelProvider
that converts a
Channel
from one voxel-type to another.Implementations of
ChannelProvider
that calculate
the gradient of a Channel
's voxels in one or more
dimensions.Implementations of
ChannelProvider
that manipulate
the intensity-values of the voxels of a Channel
's
voxels.Implementations of
ChannelProvider
that involve
conversion from or application of Mask
s.Implementations of
ChannelProvider
that involve
conversion from or application of ObjectMask
s.Implementations of
ChannelProvider
that assign a
score to particular subregions of a channel.Implementations of
ChannelProvider
that process 3D
channels slice-by-slice.Implementations of
DimensionsProvider
.Implementations of
HistogramProvider
.Implementations of
MaskProvider
.Implementations of
MaskProvider
that implement
morphological operations.Implementations of
ObjectFilter
that
independently assess each element in a collection.Implementations of
ObjectCollectionProvider
.Implementations of
BinarySegmentation
.Implementations of
StackProvider
.Implementations of
StackProvider
that color
portions of an image.Non-beans for operations or calculations relating to
Channel
s.Implementations of
ChannelProvider
that call ImageJ.Non-linear filters using ImageJ that use the statistical moments of the
intensity values in the kernel.
Non-linear filters using ImageJ that use the statistical rank of the intensity values in the
kernel.
-
Uses of ChannelProvider in org.anchoranalysis.image.bean.provider
Subclasses of ChannelProvider in org.anchoranalysis.image.bean.providerModifier and TypeClassDescriptionclass
Implementation ofChannelProvider
that calls twoChannelProvider
s that must provideChannel
s of the same dimensions.class
Implementation ofChannelProvider
that calls threeChannelProvider
s that must provideChannel
s of the same dimensions.class
Implementation ofChannelProvider
that calls a single delegateChannelProvider
.Methods in org.anchoranalysis.image.bean.provider that return ChannelProviderModifier and TypeMethodDescriptionChannelProviderUnary.getChannel()
The delegateChannelProvider
that is called.ChannelProviderBinary.getChannel1()
The first delegateChannelProvider
that is called.ChannelProviderTernary.getChannel1()
The first delegateChannelProvider
that is called.ChannelProviderBinary.getChannel2()
The second delegateChannelProvider
that is called.ChannelProviderTernary.getChannel2()
The second delegateChannelProvider
that is called.ChannelProviderTernary.getChannel3()
The third delegateChannelProvider
that is called.Methods in org.anchoranalysis.image.bean.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
ChannelProviderUnary.setChannel
(ChannelProvider channel) The delegateChannelProvider
that is called.void
ChannelProviderBinary.setChannel1
(ChannelProvider channel1) The first delegateChannelProvider
that is called.void
ChannelProviderTernary.setChannel1
(ChannelProvider channel1) The first delegateChannelProvider
that is called.void
ChannelProviderBinary.setChannel2
(ChannelProvider channel2) The second delegateChannelProvider
that is called.void
ChannelProviderTernary.setChannel2
(ChannelProvider channel2) The second delegateChannelProvider
that is called.void
ChannelProviderTernary.setChannel3
(ChannelProvider channel3) The third delegateChannelProvider
that is called. -
Uses of ChannelProvider in org.anchoranalysis.plugin.fiji.bean.channel.provider
Subclasses of ChannelProvider in org.anchoranalysis.plugin.fiji.bean.channel.providerModifier and TypeClassDescriptionclass
Performs Perona-Malik Anisotropic Diffusion.class
Applies a minimum filter to a channel using ImageJ's MinMaxMedian plugin. -
Uses of ChannelProvider in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
Modifier and TypeClassDescriptionclass
Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.class
LikeDistanceTransform3D
but applies the distance transform separately for each object in a collection. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider
Subclasses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.providerModifier and TypeClassDescriptionclass
Creates a new channel with all values initialized to a constant (by default zero)class
Creates a duplicate of the input channel.class
An abstract base class for creating a channel from specified dimensions.class
Finds the input-stack using a conventional name ofinput_image
- and extracts the first channelclass
Extracts a channel from a provider of a stack.class
Provides a channel based on a condition from a dictionary.class
Provides a channel by referencing it from a a set of named-channels.class
Takes the two channels and creates a NEW third channel whose pixels are a function of the two channelsclass
An abstract base class for creating a channel from an existing channel and a collection of objects.class
AChannelProviderUnary
which has a scalar value field.Methods in org.anchoranalysis.plugin.image.bean.channel.provider that return ChannelProviderModifier and TypeMethodDescriptionIfParamEquals.getChannelElse()
The channel provider to use if the condition is false.Methods in org.anchoranalysis.plugin.image.bean.channel.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
IfParamEquals.setChannelElse
(ChannelProvider channelElse) The channel provider to use if the condition is false. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
Modifier and TypeClassDescriptionfinal class
Adds a constant value to each voxel in a channel.class
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.class
Base class for arithmetic operations that conditionally overwrite voxel values with a constant.class
Inverts the intensity values of aChannel
by subtracting each voxel from the maximum value for the channel's data type.class
Creates a new channel by taking the maximum value of corresponding voxels from two input channels.class
Replaces voxel values with a constant value if the constant is greater than the original voxel value.class
Creates a new channel that is the mean of three input channels.class
Creates a new channel by taking the minimum value of corresponding voxels from two input channels.class
Replaces voxel values with a constant value if the constant is less than the original voxel value.class
Multiplies each voxel value in a channel by a constant value.class
Creates a new channel by multiplying corresponding voxels from two input channels.class
Subtracts each voxel value in a channel from a constant value.class
Subtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.class
Creates a new channel by subtracting corresponding voxels of the second channel from the first channel. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.assign
Modifier and TypeClassDescriptionclass
Copies the pixels fromchannelAssignFrom
tochannel
(possibly masking).class
Assigns a value from a dictionary to all voxels in a channel.class
Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target objectclass
Assigns a constant (scalar) value to the portion of the image covered by a maskMethods in org.anchoranalysis.plugin.image.bean.channel.provider.assign that return ChannelProviderModifier and TypeMethodDescriptionAssignFromChannel.getChannelAssignFrom()
The channel provider from which pixels will be assigned.Methods in org.anchoranalysis.plugin.image.bean.channel.provider.assign with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
AssignFromChannel.setChannelAssignFrom
(ChannelProvider channelAssignFrom) The channel provider from which pixels will be assigned. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.convert
Modifier and TypeClassDescriptionclass
Convert<T>
Converts a channel by applying a converter (no histogram is involved in the conversion).class
Base class for channel providers that perform conversions on a single input channel.class
Converts a channel to a different voxel data-type by applying a converter with an associated histogram. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
Modifier and TypeClassDescriptionclass
Base class to calculate the gradient of the voxels in aChannel
.class
LikeGradientBase
but allows an arbitrary constant to be added to voxels storing the gradient.class
Extracts the gradient in the direction of a particular axis (identified by an index)class
Calculates aChannel
's gradient along the x and y axes.class
3x3 Sobel Filter -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Modifier and TypeClassDescriptionclass
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)class
Creates a new channel which is a merged version of two input channels according to rules.class
Applies a median-filter with square kernelclass
Corrects a channel in the following wayclass
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128class
Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data rangeclass
Scales the channel in the X and Y dimensions.Methods in org.anchoranalysis.plugin.image.bean.channel.provider.intensity that return ChannelProviderModifier and TypeMethodDescriptionIfVoxelZero.getChannelIfVoxelZero()
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel insteadNormalizeDifferenceToMedian.getChannelLookup()
Methods in org.anchoranalysis.plugin.image.bean.channel.provider.intensity with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
IfVoxelZero.setChannelIfVoxelZero
(ChannelProvider channelIfVoxelZero) If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel insteadvoid
NormalizeDifferenceToMedian.setChannelLookup
(ChannelProvider channelLookup) -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.mask
Modifier and TypeClassDescriptionclass
class
A base class for aChannelProvider
which also uses a binary-mask, but which doesn't use any otherChannelProvider
as an input.class
A base class for aChannelProviderUnary
which also uses a binary mask.class
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.object
Modifier and TypeClassDescriptionclass
Creates a channel with a level calculated for each object using various methods.class
Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.class
Calculates a threshold-level for each object collectively based on other objects -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.score
Modifier and TypeClassDescriptionclass
Assigns a unique id number to each object.class
Creates a channel by scoring objects based on a feature calculation.class
Assigns a score (a value indicating how probable something is) to each voxelMethods in org.anchoranalysis.plugin.image.bean.channel.provider.score that return ChannelProviderMethods in org.anchoranalysis.plugin.image.bean.channel.provider.score that return types with arguments of type ChannelProviderModifier and TypeMethodDescriptionScoreVoxels.getChannelsExtra()
ScoreObjects.getListAdditionalChannelProviders()
Additional channels to be included in theEnergyStack
for feature calculation.Methods in org.anchoranalysis.plugin.image.bean.channel.provider.score with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
ScoreVoxels.setGradient
(ChannelProvider gradient) void
ScoreVoxels.setIntensity
(ChannelProvider intensity) Method parameters in org.anchoranalysis.plugin.image.bean.channel.provider.score with type arguments of type ChannelProviderModifier and TypeMethodDescriptionvoid
ScoreVoxels.setChannelsExtra
(List<ChannelProvider> channelsExtra) void
ScoreObjects.setListAdditionalChannelProviders
(List<ChannelProvider> listAdditionalChannelProviders) Additional channels to be included in theEnergyStack
for feature calculation. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.slice
Modifier and TypeClassDescriptionclass
Extracts the slice at the center (rounding down) of the range of z-stacks.class
Extracts slices fromsliceStart
(inclusive) tosliceEnd
(inclusive).class
Creates a maximum intensity projection of a 3DChannel
.class
Creates a mean intensity projection of a 3DChannel
.class
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channelMethods in org.anchoranalysis.plugin.image.bean.channel.provider.slice that return ChannelProviderMethods in org.anchoranalysis.plugin.image.bean.channel.provider.slice with parameters of type ChannelProvider -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.dimensions.provider
Methods in org.anchoranalysis.plugin.image.bean.dimensions.provider that return ChannelProviderModifier and TypeMethodDescriptionFromChannel.getChannel()
TheChannelProvider
to use for dimensions.Methods in org.anchoranalysis.plugin.image.bean.dimensions.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
FromChannel.setChannel
(ChannelProvider channel) TheChannelProvider
to use for dimensions. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.histogram.provider
Methods in org.anchoranalysis.plugin.image.bean.histogram.provider that return ChannelProviderModifier and TypeMethodDescriptionFromChannel.getChannel()
The provider for the channel from which to create the histogram.Methods in org.anchoranalysis.plugin.image.bean.histogram.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
FromChannel.setChannel
(ChannelProvider channel) The provider for the channel from which to create the histogram. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.mask.provider
Methods in org.anchoranalysis.plugin.image.bean.mask.provider that return ChannelProviderModifier and TypeMethodDescriptionFromChannelBase.getChannel()
The provider for the channel from which to create the mask.Methods in org.anchoranalysis.plugin.image.bean.mask.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
FromChannelBase.setChannel
(ChannelProvider channel) The provider for the channel from which to create the mask. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
Methods in org.anchoranalysis.plugin.image.bean.mask.provider.morphological that return ChannelProviderModifier and TypeMethodDescriptionMorphologicalOperatorBase.getBackgroundChannelProvider()
Optional provider for a background channel to use in intensity-based conditions.Methods in org.anchoranalysis.plugin.image.bean.mask.provider.morphological with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
MorphologicalOperatorBase.setBackgroundChannelProvider
(ChannelProvider backgroundChannelProvider) Optional provider for a background channel to use in intensity-based conditions. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.object.filter.independent
Methods in org.anchoranalysis.plugin.image.bean.object.filter.independent that return ChannelProviderMethods in org.anchoranalysis.plugin.image.bean.object.filter.independent with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
IntensityGreaterEqualThan.setChannel
(ChannelProvider channel) -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.object.provider
Methods in org.anchoranalysis.plugin.image.bean.object.provider that return ChannelProviderModifier and TypeMethodDescriptionUnaryWithChannelBase.getChannel()
Provider for the channel to be used in object creation.WithChannelBase.getChannel()
Provider for the channel from which objects will be created.Methods in org.anchoranalysis.plugin.image.bean.object.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
UnaryWithChannelBase.setChannel
(ChannelProvider channel) Provider for the channel to be used in object creation.void
WithChannelBase.setChannel
(ChannelProvider channel) Provider for the channel from which objects will be created. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.segment.binary
Methods in org.anchoranalysis.plugin.image.bean.segment.binary that return ChannelProviderMethods in org.anchoranalysis.plugin.image.bean.segment.binary with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
ThresholdAgainstChannel.setChannelThreshold
(ChannelProvider channelThreshold) -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.stack.provider
Methods in org.anchoranalysis.plugin.image.bean.stack.provider that return ChannelProviderModifier and TypeMethodDescriptionFromChannelOrMask.getChannel()
A channel that is provided to the stack.Methods in org.anchoranalysis.plugin.image.bean.stack.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
FromChannelOrMask.setChannel
(ChannelProvider channel) A channel that is provided to the stack.Constructors in org.anchoranalysis.plugin.image.bean.stack.provider with parameters of type ChannelProviderModifierConstructorDescriptionFromChannelOrMask
(ChannelProvider channel) Creates a new instance with a specified channel provider. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.stack.provider.color
Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color that return ChannelProviderModifier and TypeMethodDescriptionThreeChannels.getBlue()
Provider for the blue channel.ThreeChannels.getGreen()
Provider for the green channel.ThreeChannels.getRed()
Provider for the red channel.Methods in org.anchoranalysis.plugin.image.bean.stack.provider.color with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoid
ThreeChannels.setBlue
(ChannelProvider blue) Provider for the blue channel.void
ThreeChannels.setGreen
(ChannelProvider green) Provider for the green channel.void
ThreeChannels.setRed
(ChannelProvider red) Provider for the red channel. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.channel
Methods in org.anchoranalysis.plugin.image.channel with parameters of type ChannelProviderModifier and TypeMethodDescriptionstatic 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 existing channel. -
Uses of ChannelProvider in org.anchoranalysis.plugin.imagej.bean.channel.provider
Subclasses of ChannelProvider in org.anchoranalysis.plugin.imagej.bean.channel.providerModifier and TypeClassDescriptionclass
Subtracts background from a channel using ImageJ'sBackgroundSubtracter
.class
A base class for applying ImageJ rank filters to channels.class
AChannelProviderUnary
with a 'radius' parameter. -
Uses of ChannelProvider in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
-
Uses of ChannelProvider in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
Subclasses of ChannelProvider in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.momentsModifier and TypeClassDescriptionclass
Applies a 2D mean filter to a channel using ImageJ'sRankFilters
.class
Applies a 2D variance filter to a channel using ImageJ'sRankFilters
. -
Uses of ChannelProvider in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
Modifier and TypeClassDescriptionclass
Applies a 2D median filter to a channel using ImageJ'sRankFilters
.class
Applies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin.