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 Channels.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 Masks.Implementations of
ChannelProvider that involve
conversion from or application of ObjectMasks.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
Channels.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 TypeClassDescriptionclassImplementation ofChannelProviderthat calls twoChannelProviders that must provideChannels of the same dimensions.classImplementation ofChannelProviderthat calls threeChannelProviders that must provideChannels of the same dimensions.classImplementation ofChannelProviderthat calls a single delegateChannelProvider.Methods in org.anchoranalysis.image.bean.provider that return ChannelProviderModifier and TypeMethodDescriptionChannelProviderUnary.getChannel()The delegateChannelProviderthat is called.ChannelProviderBinary.getChannel1()The first delegateChannelProviderthat is called.ChannelProviderTernary.getChannel1()The first delegateChannelProviderthat is called.ChannelProviderBinary.getChannel2()The second delegateChannelProviderthat is called.ChannelProviderTernary.getChannel2()The second delegateChannelProviderthat is called.ChannelProviderTernary.getChannel3()The third delegateChannelProviderthat is called.Methods in org.anchoranalysis.image.bean.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoidChannelProviderUnary.setChannel(ChannelProvider channel) The delegateChannelProviderthat is called.voidChannelProviderBinary.setChannel1(ChannelProvider channel1) The first delegateChannelProviderthat is called.voidChannelProviderTernary.setChannel1(ChannelProvider channel1) The first delegateChannelProviderthat is called.voidChannelProviderBinary.setChannel2(ChannelProvider channel2) The second delegateChannelProviderthat is called.voidChannelProviderTernary.setChannel2(ChannelProvider channel2) The second delegateChannelProviderthat is called.voidChannelProviderTernary.setChannel3(ChannelProvider channel3) The third delegateChannelProviderthat 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 TypeClassDescriptionclassPerforms Perona-Malik Anisotropic Diffusion.classApplies 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 TypeClassDescriptionclassEuclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.classLikeDistanceTransform3Dbut 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 TypeClassDescriptionclassCreates a new channel with all values initialized to a constant (by default zero)classCreates a duplicate of the input channel.classAn abstract base class for creating a channel from specified dimensions.classFinds the input-stack using a conventional name ofinput_image- and extracts the first channelclassExtracts a channel from a provider of a stack.classProvides a channel based on a condition from a dictionary.classProvides a channel by referencing it from a a set of named-channels.classTakes the two channels and creates a NEW third channel whose pixels are a function of the two channelsclassAn abstract base class for creating a channel from an existing channel and a collection of objects.classAChannelProviderUnarywhich 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 TypeMethodDescriptionvoidIfParamEquals.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 classAdds a constant value to each voxel in a channel.classBase-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.classBase class for arithmetic operations that conditionally overwrite voxel values with a constant.classInverts the intensity values of aChannelby subtracting each voxel from the maximum value for the channel's data type.classCreates a new channel by taking the maximum value of corresponding voxels from two input channels.classReplaces voxel values with a constant value if the constant is greater than the original voxel value.classCreates a new channel that is the mean of three input channels.classCreates a new channel by taking the minimum value of corresponding voxels from two input channels.classReplaces voxel values with a constant value if the constant is less than the original voxel value.classMultiplies each voxel value in a channel by a constant value.classCreates a new channel by multiplying corresponding voxels from two input channels.classSubtracts each voxel value in a channel from a constant value.classSubtracts the mean intensity (of the entire channel or a masked portion thereof) from every voxel.classCreates 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 TypeClassDescriptionclassCopies the pixels fromchannelAssignFromtochannel(possibly masking).classAssigns a value from a dictionary to all voxels in a channel.classMatches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target objectclassAssigns 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 TypeMethodDescriptionvoidAssignFromChannel.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 TypeClassDescriptionclassConvert<T>Converts a channel by applying a converter (no histogram is involved in the conversion).classBase class for channel providers that perform conversions on a single input channel.classConverts 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 TypeClassDescriptionclassBase class to calculate the gradient of the voxels in aChannel.classLikeGradientBasebut allows an arbitrary constant to be added to voxels storing the gradient.classExtracts the gradient in the direction of a particular axis (identified by an index)classCalculates aChannel's gradient along the x and y axes.class3x3 Sobel Filter -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
Modifier and TypeClassDescriptionclassBlurs an image using a particular strategy (defaults to a gaussian blur in each slice)classCreates a new channel which is a merged version of two input channels according to rules.classApplies a median-filter with square kernelclassCorrects a channel in the following wayclassRewrites the intensity for each object-mask (assume no overlap) so that its mean is 128classChanges the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data rangeclassScales 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 TypeMethodDescriptionvoidIfVoxelZero.setChannelIfVoxelZero(ChannelProvider channelIfVoxelZero) If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel insteadvoidNormalizeDifferenceToMedian.setChannelLookup(ChannelProvider channelLookup) -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.mask
Modifier and TypeClassDescriptionclassclassA base class for aChannelProviderwhich also uses a binary-mask, but which doesn't use any otherChannelProvideras an input.classA base class for aChannelProviderUnarywhich also uses a binary mask.classSet 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 TypeClassDescriptionclassCreates a channel with a level calculated for each object using various methods.classCreates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.classCalculates 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 TypeClassDescriptionclassAssigns a unique id number to each object.classCreates a channel by scoring objects based on a feature calculation.classAssigns 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 theEnergyStackfor feature calculation.Methods in org.anchoranalysis.plugin.image.bean.channel.provider.score with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoidScoreVoxels.setGradient(ChannelProvider gradient) voidScoreVoxels.setIntensity(ChannelProvider intensity) Method parameters in org.anchoranalysis.plugin.image.bean.channel.provider.score with type arguments of type ChannelProviderModifier and TypeMethodDescriptionvoidScoreVoxels.setChannelsExtra(List<ChannelProvider> channelsExtra) voidScoreObjects.setListAdditionalChannelProviders(List<ChannelProvider> listAdditionalChannelProviders) Additional channels to be included in theEnergyStackfor feature calculation. -
Uses of ChannelProvider in org.anchoranalysis.plugin.image.bean.channel.provider.slice
Modifier and TypeClassDescriptionclassExtracts the slice at the center (rounding down) of the range of z-stacks.classExtracts slices fromsliceStart(inclusive) tosliceEnd(inclusive).classCreates a maximum intensity projection of a 3DChannel.classCreates a mean intensity projection of a 3DChannel.classCreates 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()TheChannelProviderto use for dimensions.Methods in org.anchoranalysis.plugin.image.bean.dimensions.provider with parameters of type ChannelProviderModifier and TypeMethodDescriptionvoidFromChannel.setChannel(ChannelProvider channel) TheChannelProviderto 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 TypeMethodDescriptionvoidFromChannel.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 TypeMethodDescriptionvoidFromChannelBase.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 TypeMethodDescriptionvoidMorphologicalOperatorBase.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 TypeMethodDescriptionvoidIntensityGreaterEqualThan.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 TypeMethodDescriptionvoidUnaryWithChannelBase.setChannel(ChannelProvider channel) Provider for the channel to be used in object creation.voidWithChannelBase.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 TypeMethodDescriptionvoidThresholdAgainstChannel.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 TypeMethodDescriptionvoidFromChannelOrMask.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 TypeMethodDescriptionvoidThreeChannels.setBlue(ChannelProvider blue) Provider for the blue channel.voidThreeChannels.setGreen(ChannelProvider green) Provider for the green channel.voidThreeChannels.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 ChannelDimensionsChecker.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 TypeClassDescriptionclassSubtracts background from a channel using ImageJ'sBackgroundSubtracter.classA base class for applying ImageJ rank filters to channels.classAChannelProviderUnarywith 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 TypeClassDescriptionclassApplies a 2D mean filter to a channel using ImageJ'sRankFilters.classApplies 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 TypeClassDescriptionclassApplies a 2D median filter to a channel using ImageJ'sRankFilters.classApplies a 3D median filter to a channel using a hybrid 3D median filter ImageJ plugin.