Package | Description |
---|---|
org.anchoranalysis.image.bean.channel |
Base classes for performing operations on
Channel s. |
org.anchoranalysis.image.bean.nonbean.init |
Classes that aren't AnchorBeans that pertain to the initialization of image-related beans.
|
org.anchoranalysis.image.bean.nonbean.segment |
Non-bean classes relating to image-segmentation.
|
org.anchoranalysis.image.bean.provider |
Base classes for providers of different core data entities related to images.
|
org.anchoranalysis.image.bean.threshold |
Base classes for thresholding and calculating levels for thresholding.
|
org.anchoranalysis.image.core.channel.convert.attached.histogram |
Converts a channel to another data-type based upon a
Histogram to which it is attached. |
org.anchoranalysis.image.core.object |
The key data entity
org.anchoranalysis.image.voxel.object and related-classes and
operations. |
org.anchoranalysis.image.feature.bean |
Beans pertaining to feature definition and calculation.
|
org.anchoranalysis.image.feature.bean.histogram |
Features that operate on a
Histogram . |
org.anchoranalysis.image.feature.input |
Image-related implementations of
FeatureInput . |
org.anchoranalysis.image.io.histogram.input |
Non-bean classes for reading a
Histogram from the
filesystem. |
org.anchoranalysis.image.io.histogram.output |
Non-bean classes for writing a
Histogram to the
filesystem. |
org.anchoranalysis.image.voxel.statistics |
Statistics about aggregated voxel intensities.
|
org.anchoranalysis.math.histogram |
The
Histogram data class and related operations. |
org.anchoranalysis.mpp.index |
Indexing voxel-values in different ways.
|
org.anchoranalysis.mpp.index.factory |
Factories for classes in
org.anchoranalysis.mpp.index . |
org.anchoranalysis.mpp.io.input |
Non-beans for reading data structures related to marked point processes from the file system.
|
org.anchoranalysis.plugin.fiji.bean.threshold |
Implementations of
Thresholder that use FIJI. |
org.anchoranalysis.plugin.image.bean.channel.convert |
Implementations of
ConvertChannelTo and ConvertChannelToWithHistogram . |
org.anchoranalysis.plugin.image.bean.histogram.provider |
Implementations of
HistogramProvider . |
org.anchoranalysis.plugin.image.bean.histogram.threshold |
Thresholding of intensity values represented in at
Histogram . |
org.anchoranalysis.plugin.image.feature.bean.histogram.statistic |
Implementations of
FeatureHistogram that calculate
statistics. |
org.anchoranalysis.plugin.image.feature.bean.histogram.threshold |
Implementations of
FeatureHistogram that perform
thresholding. |
org.anchoranalysis.plugin.image.feature.bean.score |
Implementations of
VoxelScore . |
org.anchoranalysis.plugin.image.feature.stack.calculation |
Implementations of
CalculationPart that process
Stack s as used by features elsewhere in this package. |
org.anchoranalysis.plugin.image.intensity |
Non-bean for operations or calculations relating to intensity.
|
org.anchoranalysis.plugin.image.intensity.level |
Non-beans for calculating a thresholding level from itensity values.
|
org.anchoranalysis.plugin.image.task.bean.grouped.histogram |
Task(s) to export histograms of intensity values.
|
org.anchoranalysis.plugin.imagej.bean.threshold |
Implementations of
Thresholder that call ImageJ. |
org.anchoranalysis.test.feature.plugins |
Testing utilities and fixtures with no greater downstream dependency than
anchor-image-feature or anchor-mpp.
|
Modifier and Type | Method and Description |
---|---|
abstract ChannelConverterAttached<Histogram,T> |
ConvertChannelToWithHistogram.createConverter()
Creates the converter.
|
Modifier and Type | Method and Description |
---|---|
NamedProviderStore<Histogram> |
ImageInitialization.histograms()
A collection of
Histogram s, indexed by name. |
Modifier and Type | Method and Description |
---|---|
Optional<Histogram> |
BinarySegmentationParameters.getIntensityHistogram()
A histogram of the intensity values of the voxels that are being segmented.
|
Constructor and Description |
---|
BinarySegmentationParameters(Optional<Histogram> intensityHistogram,
Optional<Resolution> resolution) |
BinarySegmentationParameters(Resolution resolution,
Optional<Histogram> intensityHistogram)
Creates with a specific resolution and intensity-histogram.
|
Modifier and Type | Method and Description |
---|---|
protected abstract Histogram |
HistogramProviderUnary.createFromHistogram(Histogram histogram)
Creates a
Histogram given the entity provided by the delegate. |
Histogram |
HistogramProviderUnary.get() |
Modifier and Type | Method and Description |
---|---|
protected abstract Histogram |
HistogramProviderUnary.createFromHistogram(Histogram histogram)
Creates a
Histogram given the entity provided by the delegate. |
Modifier and Type | Method and Description |
---|---|
abstract int |
CalculateLevel.calculateLevel(Histogram histogram)
Determines a voxel intensity that can be used for thresholding.
|
protected int |
CalculateLevelUnary.calculateLevelFromDelegate(Histogram histogram)
Determines a voxel intensity that can be used for thresholding from the delegate
calculateLevel . |
Modifier and Type | Method and Description |
---|---|
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 |
---|---|
void |
QuantileIntensityFromHistogram.attachObject(Histogram object) |
void |
MaxIntensityFromHistogram.attachObject(Histogram histogram) |
void |
UpperLowerQuantileIntensityFromHistogram.attachObject(Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramFromObjectsFactory.createFrom(Channel channel,
Mask mask)
|
static Histogram |
HistogramFromObjectsFactory.createFrom(Channel channel,
ObjectCollection objects)
|
static Histogram |
HistogramFromObjectsFactory.createFrom(Channel channel,
ObjectMask object)
|
static Histogram |
HistogramFromObjectsFactory.createFrom(Channel channel,
Optional<Mask> mask)
Creates a
Histogram of all voxel intensity values in channel , or only
those in mask if it is dfined. |
static Histogram |
HistogramFromObjectsFactory.createFrom(VoxelsUntyped voxels,
Optional<ObjectMask> object)
|
Modifier and Type | Method and Description |
---|---|
void |
VoxelScore.initialize(List<Histogram> histograms,
Optional<Dictionary> dictionary)
Initializes the voxels-score.
|
Modifier and Type | Method and Description |
---|---|
protected abstract double |
FeatureHistogramStatistic.calculateStatisticFrom(Histogram histogram)
Calculates the statistic from the histogram, that is subsequently returned as the
feature-value.
|
protected double |
Mean.calculateStatisticFrom(Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
Histogram |
FeatureInputHistogram.getHistogram() |
Constructor and Description |
---|
FeatureInputHistogram(Histogram histogram,
Optional<Resolution> resolution) |
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramCSVReader.readHistogramFromFile(Path filePath)
Reads a CSV file from the file-system that describes a histogram of voxel values.
|
Modifier and Type | Method and Description |
---|---|
void |
HistogramCSVGenerator.writeToFile(Histogram element,
OutputWriteSettings settings,
Path filePath) |
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramFactory.createFrom(VoxelBuffer<?> buffer)
Creates a
Histogram of the aggregated voxel intensities in a VoxelBuffer . |
static Histogram |
HistogramFactory.createFrom(VoxelsUntyped voxels)
Creates a
Histogram of the aggregated voxel intensities in a VoxelsUntyped . |
Histogram |
VoxelStatistics.histogram()
A
Histogram of all voxel values. |
Histogram |
VoxelStatisticsFromHistogram.histogram() |
Histogram |
VoxelStatisticsCombined.histogram() |
Constructor and Description |
---|
VoxelStatisticsFromHistogram(Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
Histogram |
Histogram.cropRemoveLargerValues(long maxCount)
Like
cropRemoveSmallerValues(long) but larger values are removed rather than smaller
values if the total count is too high. |
Histogram |
Histogram.cropRemoveSmallerValues(long maxCount)
Creates a
Histogram reusing the bins in the current histogram, but with an upper
limit on the total count. |
Histogram |
Histogram.duplicate()
Creates a deep-copy of the current object.
|
Histogram |
Histogram.threshold(java.util.function.DoublePredicate predicate)
Generates a new histogram containing only values that match a predicate.
|
Modifier and Type | Method and Description |
---|---|
void |
Histogram.addHistogram(Histogram other)
Adds the counts from another histogram to the current object.
|
static double |
HistogramStatistics.coefficientOfVariation(Histogram histogram)
Calculates the coefficient-of-variation of a distribution of values, represented by
their histogram.
|
static double |
HistogramStatistics.kurtosis(Histogram histogram)
Calculates the kurtosis of a distribution of values, represented by their histogram.
|
static double |
HistogramStatistics.skewness(Histogram histogram)
Calculates the skewness of a distribution of values, represented by their histogram.
|
Modifier and Type | Method and Description |
---|---|
Histogram |
VoxelPartitionHistogram.getCombined() |
Histogram |
VoxelPartitionHistogram.getSlice(int sliceID) |
Modifier and Type | Method and Description |
---|---|
void |
VoxelPartitionHistogram.cleanUp(VoxelPartitionFactory<Histogram> factory) |
Constructor and Description |
---|
VoxelPartitionHistogram(int numberSlices,
java.util.function.Supplier<Histogram> histogramFactory) |
Modifier and Type | Method and Description |
---|---|
VoxelPartition<Histogram> |
VoxelPartitonFactoryHistogram.create(int numSlices) |
Modifier and Type | Method and Description |
---|---|
void |
VoxelPartitonFactoryHistogram.addUnused(Histogram part) |
Modifier and Type | Method and Description |
---|---|
MultiInputSubMap<Histogram> |
MultiInput.histogram() |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderAutoIJ.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte binaryValues,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Modifier and Type | Method and Description |
---|---|
ChannelConverterAttached<Histogram,UnsignedByteBuffer> |
ToByteUpperLowerQuantileIntensity.createConverter() |
Modifier and Type | Method and Description |
---|---|
Histogram |
CutBelowThreshold.createFromHistogram(Histogram histogram) |
Histogram |
GreaterThanThreshold.createFromHistogram(Histogram histogram) |
Histogram |
Reference.get() |
Histogram |
FromChannel.get() |
Modifier and Type | Method and Description |
---|---|
Histogram |
CutBelowThreshold.createFromHistogram(Histogram histogram) |
Histogram |
GreaterThanThreshold.createFromHistogram(Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
int |
Minimum.calculateLevel(Histogram h) |
int |
EmptyHistogramConstant.calculateLevel(Histogram histogram) |
int |
OtsuWeighted.calculateLevel(Histogram histogram) |
int |
Quantile.calculateLevel(Histogram histogram) |
int |
Maximum.calculateLevel(Histogram h) |
int |
Constant.calculateLevel(Histogram histogram) |
int |
Otsu.calculateLevel(Histogram histogram) |
int |
CalculateLevelRelativeToThreshold.calculateLevel(Histogram histogram) |
int |
ClampHistogramMax.calculateLevel(Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
protected double |
Skewness.calculateStatisticFrom(Histogram histogram) |
protected double |
Minimum.calculateStatisticFrom(Histogram histogram) |
protected double |
Kurtosis.calculateStatisticFrom(Histogram histogram) |
protected double |
CoefficientOfVariation.calculateStatisticFrom(Histogram histogram) |
protected double |
TotalCount.calculateStatisticFrom(Histogram histogram) |
protected double |
Count.calculateStatisticFrom(Histogram histogram) |
protected double |
Quantile.calculateStatisticFrom(Histogram histogram) |
protected double |
Variance.calculateStatisticFrom(Histogram histogram) |
protected double |
Maximum.calculateStatisticFrom(Histogram histogram) |
protected double |
Mode.calculateStatisticFrom(Histogram histogram) |
protected double |
Range.calculateStatisticFrom(Histogram histogram) |
protected double |
StandardDeviation.calculateStatisticFrom(Histogram histogram) |
protected double |
MeanRaisedToPower.calculateStatisticFrom(Histogram histogram) |
protected double |
RatioNonMode.calculateStatisticFrom(Histogram histogram) |
protected double |
NumberDistinctValues.calculateStatisticFrom(Histogram histogram) |
protected double |
Median.calculateStatisticFrom(Histogram histogram) |
protected double |
Sum.calculateStatisticFrom(Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
protected double |
RatioThreshold.calculateStatisticFrom(Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
protected void |
CalculateLevel.beforeCalcSetup(Histogram histogram,
int level) |
protected abstract void |
CalculateLevelBase.beforeCalcSetup(Histogram histogram,
int level) |
protected void |
DifferenceCalculateLevelStandardDeviation.beforeCalcSetup(Histogram histogram,
int level) |
Modifier and Type | Method and Description |
---|---|
void |
NormalizeByMax.initialize(List<Histogram> histograms,
Optional<Dictionary> dictionary) |
void |
CalculateLevelBase.initialize(List<Histogram> histograms,
Optional<Dictionary> dictionary) |
void |
FromDictionaryBase.initialize(List<Histogram> histograms,
Optional<Dictionary> dictionary) |
void |
IdentityImposeValueRelationToHistogram.initialize(List<Histogram> histograms,
Optional<Dictionary> dictionary) |
Modifier and Type | Method and Description |
---|---|
protected Histogram |
CalculateHistogram.execute(FeatureInputStack input) |
protected Histogram |
CalculateHistogramMasked.execute(FeatureInputStack input) |
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramThresholder.withCalculateLevel(Histogram histogram,
CalculateLevel calculateLevel)
Retains the portion of the histogram greater or equal to the calculated-level.
|
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramThresholder.withCalculateLevel(Histogram histogram,
CalculateLevel calculateLevel)
Retains the portion of the histogram greater or equal to the calculated-level.
|
Modifier and Type | Method and Description |
---|---|
Histogram |
LevelResult.getHistogram() |
Constructor and Description |
---|
LevelResult(int level,
ObjectMask object,
Histogram histogram) |
Modifier and Type | Method and Description |
---|---|
protected CheckedFunction<Channel,Histogram,CreateException> |
ExportImageHistograms.createChannelDeriver(ChannelSource source) |
protected GroupMapByName<Histogram,Histogram> |
ExportImageHistograms.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext) |
protected GroupMapByName<Histogram,Histogram> |
ExportImageHistograms.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext) |
Modifier and Type | Method and Description |
---|---|
protected void |
ExportImageHistograms.processIndividual(String name,
Histogram individual,
boolean partOfGroup,
CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected void |
ExportImageHistograms.processIndividual(String name,
Histogram individual,
boolean partOfGroup,
CheckedBiConsumer<String,Histogram,OperationFailedException> consumeIndividual,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
BinaryVoxels<UnsignedByteBuffer> |
ThresholderSimpleFillHoles2D.threshold(VoxelsUntyped inputBuffer,
BinaryValuesByte bvOut,
Optional<Histogram> histogram,
Optional<ObjectMask> objectMask) |
Modifier and Type | Method and Description |
---|---|
static Histogram |
HistogramFixture.createAscending()
a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count
5, value 100 has count 100 etc.)
|
static Histogram |
HistogramFixture.createDescending() |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.