Modifier and Type | Method and Description |
---|---|
Channel |
EnergyStackWithoutParameters.getChannel(int index)
Returns the channel at a particular position in the stack.
|
Channel |
EnergyStack.getChannel(int index)
Returns the channel at a particular position in the stack.
|
Constructor and Description |
---|
EnergyStack(Channel channel)
Create from a single
Channel . |
EnergyStackWithoutParameters(Channel channel)
Create a energy-stack comprised of a single channel
|
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelAggregator.aggregatedChannel()
Retrieve or create a
Channel with containing the aggregated values. |
protected abstract Channel |
ChannelAggregator.retrieveCreateAggregatedChannel()
Retrieve or create an aggregated-channel of type
outputType . |
Modifier and Type | Method and Description |
---|---|
void |
ChannelAggregator.addChannel(Channel channel,
Logger logger)
Adds a
Channel to the aggregation. |
protected abstract void |
ChannelAggregator.addChannelAfterCheck(Channel channel)
Adds a
Channel to the aggregation - after checking channel has acceptable
dimensions. |
Modifier and Type | Method and Description |
---|---|
protected abstract ChannelConverterAttached<Channel,UnsignedByteBuffer> |
StackDisplayer.createConverterFor(VoxelDataType dataType)
Determines what kind of converter to use for a particular channel, to map it to an unsigned
8-bit channel.
|
protected ChannelConverterAttached<Channel,UnsignedByteBuffer> |
IntensityQuantiles.createConverterFor(VoxelDataType dataType) |
Modifier and Type | Method and Description |
---|---|
DisplayStack |
StackDisplayer.deriveFrom(Channel channel)
Creates from a
Channel . |
Modifier and Type | Method and Description |
---|---|
void |
ConsistentChannelChecker.checkChannelType(Channel channel)
Checks that a channel has the same type (max value) as the others.
|
Modifier and Type | Method and Description |
---|---|
NamedProviderStore<Channel> |
ImageInitialization.channels()
A collection of
Channel s, indexed by name. |
Modifier and Type | Method and Description |
---|---|
protected abstract Channel |
ChannelProviderUnary.createFromChannel(Channel channel)
Creates a
Channel given the entity provided by the delegate. |
Channel |
ChannelProviderBinary.get() |
Channel |
ChannelProviderTernary.get() |
Channel |
ChannelProviderUnary.get() |
protected abstract Channel |
ChannelProviderBinary.process(Channel channel1,
Channel channel2)
Creates a
Channel given the two entities provided by the delegates. |
protected abstract Channel |
ChannelProviderTernary.process(Channel channel1,
Channel channel2,
Channel channel3)
Creates a
Channel given the two entities provided by the delegates. |
Modifier and Type | Method and Description |
---|---|
protected abstract Channel |
ChannelProviderUnary.createFromChannel(Channel channel)
Creates a
Channel given the entity provided by the delegate. |
protected abstract Channel |
ChannelProviderBinary.process(Channel channel1,
Channel channel2)
Creates a
Channel given the two entities provided by the delegates. |
protected abstract Channel |
ChannelProviderTernary.process(Channel channel1,
Channel channel2,
Channel channel3)
Creates a
Channel given the two entities provided by the delegates. |
Modifier and Type | Method and Description |
---|---|
protected static void |
SegmentChannelIntoObjects.checkUnsupported3D(Channel channel)
Throws an exception if the channel has more than one z-slice, as 3D is unsupported by the
implementation.
|
ObjectCollection |
SegmentChannelIntoObjectsUnary.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds) |
abstract ObjectCollection |
SegmentChannelIntoObjects.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds)
Segments a channel to produce an object-collection.
|
protected abstract ObjectCollection |
SegmentChannelIntoObjectsUnary.segment(Channel channel,
Optional<ObjectMask> object,
Optional<ObjectCollection> seeds,
SegmentChannelIntoObjects upstreamSegmenter)
Creates an
ObjectCollection given the segmentation-results provided by the delegate. |
Modifier and Type | Method and Description |
---|---|
Channel |
Channel.duplicate()
A deep-copy.
|
Channel |
Channel.extractSlice(int sliceIndex)
Creates a new
Channel containing only one particular slice. |
Channel |
Channel.projectMax()
A maximum-intensity
projection across the z-slices.
|
Channel |
Channel.projectMean()
A mean-intensity projection across the z-slices.
|
Channel |
Channel.resizeXY(Extent extentToAssign,
VoxelsResizer resizer)
Resizes the dimensions of the channel, interpolating the existing voxel values to match.
|
Channel |
Channel.resizeXY(int x,
int y,
VoxelsResizer resizer)
Like
resizeXY(Extent, VoxelsResizer) but specifies the size via int
parameters. |
Channel |
Channel.scaleXY(ScaleFactor scaleFactor,
VoxelsResizer resizer)
Resizes the dimensions of the channel, by scaling the existing size by a factor.
|
Modifier and Type | Method and Description |
---|---|
boolean |
Channel.equalsDeep(Channel other,
boolean compareResolution)
Are the two channels equal using a deep voxel by voxel comparison?
|
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelConverter.convert(Channel channel,
ConversionPolicy changeExisting)
Converts
channel to have voxels with data-type T . |
Channel |
ChannelConverterMulti.convert(Channel channel,
VoxelDataType outputVoxelType)
Converts a
Channel 's voxels to another type. |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelConverter.convert(Channel channel,
ConversionPolicy changeExisting)
Converts
channel to have voxels with data-type T . |
Channel |
ChannelConverterMulti.convert(Channel channel,
VoxelDataType outputVoxelType)
Converts a
Channel 's voxels to another type. |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelConverterAttached.convert(Channel channel,
ConversionPolicy changeExisting)
Converts the voxel-type in a
Channel . |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelConverterAttached.convert(Channel channel,
ConversionPolicy changeExisting)
Converts the voxel-type in a
Channel . |
Modifier and Type | Method and Description |
---|---|
Channel |
IntensityRange.convert(Channel channel,
ConversionPolicy changeExisting) |
Channel |
MaxIntensity.convert(Channel channel,
ConversionPolicy changeExisting) |
Modifier and Type | Method and Description |
---|---|
void |
IntensityRange.attachObject(Channel channel) |
void |
MaxIntensity.attachObject(Channel channel) |
Channel |
IntensityRange.convert(Channel channel,
ConversionPolicy changeExisting) |
Channel |
MaxIntensity.convert(Channel channel,
ConversionPolicy changeExisting) |
Modifier and Type | Method and Description |
---|---|
Channel |
QuantileIntensityFromHistogram.convert(Channel channel,
ConversionPolicy changeExisting) |
Channel |
MaxIntensityFromHistogram.convert(Channel channel,
ConversionPolicy changeExisting) |
Channel |
UpperLowerQuantileIntensityFromHistogram.convert(Channel channel,
ConversionPolicy changeExisting) |
Modifier and Type | Method and Description |
---|---|
Channel |
QuantileIntensityFromHistogram.convert(Channel channel,
ConversionPolicy changeExisting) |
Channel |
MaxIntensityFromHistogram.convert(Channel channel,
ConversionPolicy changeExisting) |
Channel |
UpperLowerQuantileIntensityFromHistogram.convert(Channel channel,
ConversionPolicy changeExisting) |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFactory.create(Dimensions dimensions,
VoxelDataType channelDataType)
Creates an empty initialized channel for a particular data-type.
|
Channel |
ChannelFactory.create(Voxels<?> voxels)
Create a
Channel from particular voxels. |
Channel |
ChannelFactory.create(Voxels<?> voxels,
Optional<Resolution> resolution)
Create a
Channel from particular voxels. |
Channel |
ChannelFactorySingleType.create(Voxels<?> voxels,
Optional<Resolution> resolution)
Create a
Channel from voxels and a resolution. |
Channel |
ChannelFactorySingleType.createEmptyInitialised(Dimensions dimensions)
Create a
Channel initialized with zero-valued voxel-buffers. |
Channel |
ChannelFactory.createEmptyInitialisedToSupportMaxValue(Dimensions dimensions,
long maxIntensityValueNeeded)
Creates an empty initialized channel with discrete type with as minimal as needed data-type
to support a maximum value.
|
Channel |
ChannelFactorySingleType.createEmptyUninitialised(Dimensions dimensions)
Create a
Channel without initialization with voxel-buffers. |
Channel |
ChannelFactory.createUninitialised(Dimensions dimensions,
VoxelDataType channelDataType)
Create a
Channel without initialization with voxel-buffers. |
Modifier and Type | Method and Description |
---|---|
Channel |
Mask.channel()
The underlying channel which contains the binary-values.
|
Constructor and Description |
---|
Mask(Channel channel)
Creates a mask from an existing channel using default values for off (0) and on
(255).
|
Mask(Channel channel,
BinaryValuesInt binaryValues)
Creates a mask from an existing channel.
|
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. |
Modifier and Type | Method and Description |
---|---|
Channel |
LabelObjects.createLabelledChannel(BoundedList<T> elements,
Optional<Map<Integer,T>> mapLabels)
Creates a channel that contains a unique integer (label) for each element's
object-representation.
|
Modifier and Type | Method and Description |
---|---|
void |
LabelObjects.labelElements(Channel channel,
Iterable<T> elements,
Optional<Map<Integer,T>> mapLabels)
Replaces the contents of the channel so that all element's voxels are labelled with
successive unique integer identifiers 1,2,3 etc.
|
Modifier and Type | Method and Description |
---|---|
Channel |
RGBStack.blue()
The blue channel.
|
Channel |
DisplayStack.createChannel(int index,
boolean alwaysNew)
Create
Channel for a particular index after applying conversion. |
Channel |
DisplayStack.extractChannelForBoundingBox(int index,
BoundingBox box)
|
Channel |
StackNotUniformSized.getChannel(int index)
Returns the channel at a particular position in the stack.
|
Channel |
RGBStack.getChannel(int index)
Returns the channel at a particular position in the stack.
|
Channel |
Stack.getChannel(int index)
Returns the channel at a particular position in the stack.
|
Channel |
RGBStack.green()
The green channel.
|
Channel |
RGBStack.red()
The red channel.
|
Modifier and Type | Method and Description |
---|---|
List<Channel> |
Stack.asListChannels()
|
List<Optional<ChannelConverterAttached<Channel,UnsignedByteBuffer>>> |
DisplayStack.getConverters()
A list of optional converters that will be applied to the respective channel in
stack
if they exist. |
Iterator<Channel> |
StackNotUniformSized.iterator() |
Iterator<Channel> |
RGBStack.iterator() |
Iterator<Channel> |
Stack.iterator() |
Modifier and Type | Method and Description |
---|---|
void |
StackNotUniformSized.addChannel(Channel channel)
Appends a channel to the stack, as the new final-most channel position-wise.
|
void |
Stack.addChannel(Channel channel)
Appends a channel to the stack, as the new final-most channel position-wise.
|
Constructor and Description |
---|
RGBStack(Channel red,
Channel green,
Channel blue)
Create with
Channel s for each color. |
Stack(boolean rgb,
Channel... channels)
Creates from a varying number of channels, and a flag to indicate if they represent an RGB
image or not.
|
Stack(Channel channel)
Creates a
Stack with a single channel. |
StackNotUniformSized(Channel channel)
Creates from a single
Channel . |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelGetter.getChannel(String channelName,
int timeIndex,
Logger logger)
Retrieve the
Channel corresponding to channelName at a particular time-frame. |
Modifier and Type | Method and Description |
---|---|
Channel |
OpenedNamedChannels.getChannel(String channelName,
int timeIndex,
Logger logger) |
Channel |
NamedChannelsConcatenate.getChannel(String channelName,
int timeIndex,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
Optional<Channel> |
OpenedNamedChannels.getChannelOptional(String channelName,
int timeIndex,
Logger logger) |
Optional<Channel> |
NamedChannelsConcatenate.getChannelOptional(String channelName,
int timeIndex,
Logger logger) |
Optional<Channel> |
NamedChannelsMap.getChannelOptional(String channelName,
int timeIndex,
Logger logger)
Gets a channel if it exists, returning empty if it doesn't.
|
Modifier and Type | Method and Description |
---|---|
Stack |
ChannelGenerator.transform(Channel element) |
Modifier and Type | Method and Description |
---|---|
Channel |
DestinationChannelForIndex.get(int index) |
Modifier and Type | Method and Description |
---|---|
static void |
CopyConvert.copyAllFrames(loci.formats.IFormatReader reader,
List<Channel> destination,
ImageFileShape targetShape,
ConvertTo<?> convertTo,
ReadOptions readOptions,
OrientationChange orientationCorrection)
Copies all frames, channels, z-slices (in a byte-array) into a destination set of
Channel s converting them if necessary along the way. |
Modifier and Type | Method and Description |
---|---|
static Channel |
ConvertFromImagePlus.toChannel(ij.ImagePlus imagePlus,
Optional<Resolution> resolution)
Converts an
ImagePlus to a Channel . |
Modifier and Type | Method and Description |
---|---|
static ij.ImagePlus |
ConvertToImagePlus.from(Channel channel)
Creates an
ImagePlus from a Channel . |
Modifier and Type | Method and Description |
---|---|
Channel |
AnisotropicDiffusion.createFromChannel(Channel channel) |
Channel |
MinimumFilter.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
AnisotropicDiffusion.createFromChannel(Channel channel) |
Channel |
MinimumFilter.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
protected Channel |
DistanceTransformForEachObject3D.createFromDimensions(Dimensions dimensions) |
protected Channel |
DistanceTransform3D.createFromMask(Mask mask) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
AutoLocalThreshold.createFromSource(Channel channel) |
Modifier and Type | Method and Description |
---|---|
protected Channel |
ProjectableBufferAggregator.retrieveCreateAggregatedChannel() |
Modifier and Type | Method and Description |
---|---|
protected void |
ProjectableBufferAggregator.addChannelAfterCheck(Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
UnaryWithObjectsBase.createFromChannel(Channel channel) |
Channel |
IfParamEquals.createFromChannel(Channel channel) |
protected Channel |
Duplicate.createFromChannel(Channel channel) |
Channel |
UnaryWithValueBase.createFromChannel(Channel channel) |
protected abstract Channel |
UnaryWithObjectsBase.createFromChannel(Channel channel,
ObjectCollection objects) |
protected abstract Channel |
UnaryWithValueBase.createFromChannelWithConstant(Channel channel,
double value) |
protected abstract Channel |
FromDimensionsBase.createFromDimensions(Dimensions dimensions) |
protected Channel |
CreateNew.createFromDimensions(Dimensions dimensions) |
Channel |
FromStack.get() |
Channel |
Reference.get() |
Channel |
FromInput.get() |
Channel |
FromDimensionsBase.get() |
protected Channel |
TwoVoxelMappingBase.process(Channel channel1,
Channel channel2) |
Modifier and Type | Method and Description |
---|---|
Channel |
UnaryWithObjectsBase.createFromChannel(Channel channel) |
Channel |
IfParamEquals.createFromChannel(Channel channel) |
protected Channel |
Duplicate.createFromChannel(Channel channel) |
Channel |
UnaryWithValueBase.createFromChannel(Channel channel) |
protected abstract Channel |
UnaryWithObjectsBase.createFromChannel(Channel channel,
ObjectCollection objects) |
protected abstract Channel |
UnaryWithValueBase.createFromChannelWithConstant(Channel channel,
double value) |
protected Channel |
TwoVoxelMappingBase.process(Channel channel1,
Channel channel2) |
Modifier and Type | Method and Description |
---|---|
Channel |
Invert.createFromChannel(Channel channel) |
Channel |
ArithmeticWithConstantConditionallyWriteBase.createFromChannelWithConstant(Channel channel,
double value) |
Channel |
ArithmeticWithConstantBase.createFromChannelWithConstant(Channel channel,
double value) |
protected Channel |
SubtractMean.createFromMaskedChannel(Channel channel,
Mask mask) |
protected Channel |
MeanThreeChannels.process(Channel channel1,
Channel channel2,
Channel channel3) |
Modifier and Type | Method and Description |
---|---|
Channel |
Invert.createFromChannel(Channel channel) |
Channel |
ArithmeticWithConstantConditionallyWriteBase.createFromChannelWithConstant(Channel channel,
double value) |
Channel |
ArithmeticWithConstantBase.createFromChannelWithConstant(Channel channel,
double value) |
protected Channel |
SubtractMean.createFromMaskedChannel(Channel channel,
Mask mask) |
protected Channel |
MeanThreeChannels.process(Channel channel1,
Channel channel2,
Channel channel3) |
Modifier and Type | Method and Description |
---|---|
Channel |
AssignFromIntersectingObjects.createFromChannel(Channel channel) |
Channel |
AssignFromDictionary.createFromChannel(Channel channel) |
protected Channel |
AssignValue.createFromMaskedChannel(Channel channel,
Mask mask) |
protected Channel |
AssignFromChannel.createFromMaskedChannel(Channel channel,
Mask mask) |
Modifier and Type | Method and Description |
---|---|
Channel |
AssignFromIntersectingObjects.createFromChannel(Channel channel) |
Channel |
AssignFromDictionary.createFromChannel(Channel channel) |
protected Channel |
AssignValue.createFromMaskedChannel(Channel channel,
Mask mask) |
protected Channel |
AssignFromChannel.createFromMaskedChannel(Channel channel,
Mask mask) |
Modifier and Type | Method and Description |
---|---|
Channel |
ConvertWithHistogram.createFromChannel(Channel channel) |
Channel |
Convert.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
ConvertWithHistogram.createFromChannel(Channel channel) |
Channel |
Convert.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
protected Channel |
GradientBase.convertToOutputType(Channel channelToConvert) |
Channel |
Sobel.createFromChannel(Channel channelIn) |
Channel |
GradientBaseAddSum.createFromChannel(Channel channelIn) |
Modifier and Type | Method and Description |
---|---|
protected Channel |
GradientBase.convertToOutputType(Channel channelToConvert) |
Channel |
Sobel.createFromChannel(Channel channelIn) |
Channel |
GradientBaseAddSum.createFromChannel(Channel channelIn) |
Modifier and Type | Method and Description |
---|---|
Channel |
QuantileStretch.createFromChannel(Channel channel) |
Channel |
ScaleXY.createFromChannel(Channel channel) |
Channel |
Blur.createFromChannel(Channel channel) |
Channel |
IfVoxelZero.createFromChannel(Channel channel) |
Channel |
Median.createFromChannel(Channel channel) |
protected Channel |
NormalizeObjectIntensity.createFromChannel(Channel channel,
ObjectCollection objects) |
protected Channel |
NormalizeDifferenceToMedian.createFromChannel(Channel channel,
ObjectCollection objects) |
static Channel |
IfVoxelZero.mergeViaZeroCheck(Channel channel,
Channel channelIfPixelZero,
VoxelDataType combinedType,
double multiplierIfNonZero)
Creates a new channel which is a merged version of two input channels according to rules.
|
Modifier and Type | Method and Description |
---|---|
Channel |
QuantileStretch.createFromChannel(Channel channel) |
Channel |
ScaleXY.createFromChannel(Channel channel) |
Channel |
Blur.createFromChannel(Channel channel) |
Channel |
IfVoxelZero.createFromChannel(Channel channel) |
Channel |
Median.createFromChannel(Channel channel) |
protected Channel |
NormalizeObjectIntensity.createFromChannel(Channel channel,
ObjectCollection objects) |
protected Channel |
NormalizeDifferenceToMedian.createFromChannel(Channel channel,
ObjectCollection objects) |
static Channel |
IfVoxelZero.mergeViaZeroCheck(Channel channel,
Channel channelIfPixelZero,
VoxelDataType combinedType,
double multiplierIfNonZero)
Creates a new channel which is a merged version of two input channels according to rules.
|
Modifier and Type | Method and Description |
---|---|
Channel |
UnaryWithMaskBase.createFromChannel(Channel channel) |
protected abstract Channel |
FromMaskBase.createFromMask(Mask mask) |
protected Channel |
FromMask.createFromMask(Mask mask) |
protected abstract Channel |
UnaryWithMaskBase.createFromMaskedChannel(Channel channel,
Mask mask) |
protected Channel |
ZeroOutsideMask.createFromMaskedChannel(Channel channel,
Mask mask) |
Channel |
FromMaskBase.get() |
Modifier and Type | Method and Description |
---|---|
Channel |
UnaryWithMaskBase.createFromChannel(Channel channel) |
protected abstract Channel |
UnaryWithMaskBase.createFromMaskedChannel(Channel channel,
Mask mask) |
protected Channel |
ZeroOutsideMask.createFromMaskedChannel(Channel channel,
Mask mask) |
Modifier and Type | Method and Description |
---|---|
Channel |
LevelPerObjectBase.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
LevelPerObjectBase.createFromChannel(Channel channel) |
protected void |
LevelPerObjectNeighbors.writeLevelsForObjects(Channel channelIntensity,
ObjectCollection objects,
Channel output) |
protected void |
LevelPerObjectIndependently.writeLevelsForObjects(Channel channelIntensity,
ObjectCollection objects,
Channel output) |
protected abstract void |
LevelPerObjectBase.writeLevelsForObjects(Channel input,
ObjectCollection objects,
Channel output)
Creates a channel with the levels for a set of objects
|
Modifier and Type | Method and Description |
---|---|
protected Channel |
IdentifyObjects.createFromChannel(Channel channel,
ObjectCollection objects) |
protected Channel |
ScoreObjects.createFromChannel(Channel channel,
ObjectCollection objects) |
Channel |
ScoreVoxels.get() |
Modifier and Type | Method and Description |
---|---|
protected Channel |
IdentifyObjects.createFromChannel(Channel channel,
ObjectCollection objects) |
protected Channel |
ScoreObjects.createFromChannel(Channel channel,
ObjectCollection objects) |
Modifier and Type | Method and Description |
---|---|
Channel |
MeanIntensityProjection.createFromChannel(Channel channel) |
Channel |
MaximumIntensityProjection.createFromChannel(Channel channel) |
Channel |
ExtractCenterSlice.createFromChannel(Channel channel) |
Channel |
ExtractSliceRange.createFromChannel(Channel channel) |
protected Channel |
RepeatSlice.createFromDimensions(Dimensions dimensions) |
Modifier and Type | Method and Description |
---|---|
Channel |
MeanIntensityProjection.createFromChannel(Channel channel) |
Channel |
MaximumIntensityProjection.createFromChannel(Channel channel) |
Channel |
ExtractCenterSlice.createFromChannel(Channel channel) |
Channel |
ExtractSliceRange.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
protected abstract Mask |
FromChannelBase.createFromSource(Channel source) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
FromChannel.createFromSource(Channel source) |
Modifier and Type | Method and Description |
---|---|
protected Mask |
SegmentChannel.createFromSource(Channel source) |
protected Mask |
Threshold.createFromSource(Channel source) |
Modifier and Type | Method and Description |
---|---|
protected abstract ObjectCollection |
WithChannelBase.createFromChannel(Channel channelSrc) |
protected abstract ObjectCollection |
UnaryWithChannelBase.createFromObjects(ObjectCollection objectsSource,
Channel channelSource) |
Modifier and Type | Method and Description |
---|---|
protected ObjectCollection |
SegmentChannel.createFromChannel(Channel channelSource) |
protected ObjectCollection |
SegmentWithSeeds.createFromChannel(Channel channel) |
ObjectCollection |
SegmentChannelByObject.createFromObjects(ObjectCollection objectsSource,
Channel channelToSegment) |
protected ObjectCollection |
BinarySegmentByObject.createFromObjects(ObjectCollection objectsSource,
Channel channelSource) |
Modifier and Type | Method and Description |
---|---|
abstract Channel |
MinimaImposition.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
Channel |
MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
abstract Channel |
MinimaImposition.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
Channel |
MinimaImpositionGrayscaleReconstruction.imposeMinima(Channel channel,
ObjectCollection seeds,
Optional<ObjectMask> containingMask) |
Modifier and Type | Method and Description |
---|---|
ObjectCollection |
WatershedYeong.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds) |
Modifier and Type | Method and Description |
---|---|
static Stack |
ThreeChannels.createRGBStack(Channel channelRed,
Channel channelGreen,
Channel channelBlue,
VoxelDataType outputType) |
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 | Method and Description |
---|---|
static void |
DimensionsChecker.check(Channel channel,
Mask mask) |
static void |
DimensionsChecker.check(Channel channelToCheck,
String channelToCheckName,
Dimensions dimFromChannel)
Checks a channel to make sure it's the same size as an an existing channel.
|
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.
|
static Mask |
DimensionsChecker.createSameSize(MaskProvider 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 | Method and Description |
---|---|
protected abstract double |
SpecificEnergyChannelBase.calculateWithChannel(ObjectMask object,
Channel channel) |
protected double |
CountEqual.calculateWithChannel(ObjectMask object,
Channel channel) |
Modifier and Type | Method and Description |
---|---|
protected double |
TextureScore.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input,
Channel channel) |
protected double |
IntensityMeanMaxSlice.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input,
Channel channel) |
protected double |
Intensity.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input,
Channel channel) |
protected double |
IntensityMeanShellBase.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input,
Channel channel) |
protected abstract double |
FeatureEnergyChannel.calculateForChannel(FeatureCalculationInput<FeatureInputSingleObject> input,
Channel channel) |
protected double |
IntensityMeanShellMaxSlice.calculateForShell(ObjectMask object,
Channel channel) |
protected double |
IntensityMeanShell.calculateForShell(ObjectMask object,
Channel channel) |
protected abstract double |
IntensityMeanShellBase.calculateForShell(ObjectMask shell,
Channel channel) |
Modifier and Type | Method and Description |
---|---|
static double |
IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel,
ObjectMask object) |
static double |
IntensityMeanCalculator.calculateMeanIntensityObject(Channel channel,
ObjectMask object,
boolean excludeZero) |
Modifier and Type | Method and Description |
---|---|
static LevelResultCollection |
LevelResultCollectionFactory.createCollection(Channel channel,
ObjectCollection objects,
CalculateLevel calculateLevel,
int numDilations,
MessageLogger logger) |
Modifier and Type | Method and Description |
---|---|
protected CheckedFunction<Channel,Channel,CreateException> |
AggregateChannelTask.createChannelDeriver(ChannelSource source) |
protected CheckedFunction<Channel,Channel,CreateException> |
AggregateChannelTask.createChannelDeriver(ChannelSource source) |
protected GroupMapByName<Channel,ChannelAggregator> |
AggregateChannelTask.createGroupMap(ConsistentChannelChecker channelChecker,
Optional<java.util.stream.Stream<String>> groupIdentifiers,
Optional<InputOutputContext> outputContext,
OperationContext operationContext) |
Modifier and Type | Method and Description |
---|---|
protected void |
AggregateChannelTask.processIndividual(String name,
Channel individual,
boolean partOfGroup,
CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected void |
AggregateChannelTask.processIndividual(String name,
Channel individual,
boolean partOfGroup,
CheckedBiConsumer<String,Channel,OperationFailedException> consumeIndividual,
InputOutputContext context) |
Modifier and Type | Method and Description |
---|---|
protected abstract CheckedFunction<Channel,S,CreateException> |
GroupedStackBase.createChannelDeriver(ChannelSource source)
A function to derive the individual type used for aggregation from a
Channel . |
Modifier and Type | Method and Description |
---|---|
protected CheckedFunction<Channel,Histogram,CreateException> |
ExportImageHistograms.createChannelDeriver(ChannelSource source) |
Modifier and Type | Method and Description |
---|---|
Iterator<Map.Entry<String,Channel>> |
NamedChannels.iterator() |
Modifier and Type | Method and Description |
---|---|
void |
NamedChannels.add(String name,
Channel channel)
Adds a
Channel with a name. |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelSource.extractChannel(Stack stack,
boolean checkType,
int index) |
Channel |
ChannelSource.extractChannel(String stackName,
boolean checkType)
|
Channel |
ChannelSource.extractChannel(String stackName,
boolean checkType,
int index) |
Channel |
NamedChannel.getChannel() |
Constructor and Description |
---|
NamedChannel(String name,
Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelGetterForTimepoint.getChannel(String channelName,
Logger logger) |
Modifier and Type | Method and Description |
---|---|
Channel |
WithRadiusBase.createFromChannel(Channel channel) |
protected abstract Channel |
WithRadiusBase.createFromChannel(Channel channel,
int radius) |
Channel |
WithFilterBase.createFromChannel(Channel channel,
int radius) |
protected Channel |
BackgroundSubtractor.createFromChannel(Channel channel,
int radius) |
Modifier and Type | Method and Description |
---|---|
Channel |
WithRadiusBase.createFromChannel(Channel channel) |
protected abstract Channel |
WithRadiusBase.createFromChannel(Channel channel,
int radius) |
Channel |
WithFilterBase.createFromChannel(Channel channel,
int radius) |
protected Channel |
BackgroundSubtractor.createFromChannel(Channel channel,
int radius) |
Modifier and Type | Method and Description |
---|---|
Channel |
GaussianBlur2D.createFromChannel(Channel channel) |
Channel |
EdgeFilterIJ.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
GaussianBlur2D.createFromChannel(Channel channel) |
Channel |
EdgeFilterIJ.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
MedianFilter3D.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
MedianFilter3D.createFromChannel(Channel channel) |
Modifier and Type | Method and Description |
---|---|
ObjectCollection |
FloodFillEachIntensityLevel.segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds) |
Modifier and Type | Method and Description |
---|---|
static Channel |
FilterHelper.applyRankFilter(Channel channel,
int radius,
int filterType)
Applies a 2D rank-filter to each slice independently.
|
Modifier and Type | Method and Description |
---|---|
static Channel |
FilterHelper.applyRankFilter(Channel channel,
int radius,
int filterType)
Applies a 2D rank-filter to each slice independently.
|
static void |
FilterHelper.processEachSlice(Channel channel,
java.util.function.Consumer<ij.process.ImageProcessor> consumer)
|
Modifier and Type | Method and Description |
---|---|
Channel |
ChannelFixture.createChannel(Extent extent,
ChannelFixture.IntensityFunction createIntensity,
VoxelDataType channelVoxelType) |
Modifier and Type | Method and Description |
---|---|
void |
WriteIntoDirectory.writeChannel(String outputName,
Channel channel) |
Modifier and Type | Method and Description |
---|---|
Channel |
TestLoaderImage.openChannelFromFilePath(Path filePath) |
Channel |
TestLoaderImage.openChannelFromTestPath(String testPath) |
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.