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gselzergselzer
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Opify labeling package
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‎src/main/java/net/imglib2/algorithm/labeling/ConnectedComponentAnalysis.java

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@@ -117,6 +117,7 @@ public static < T > ToLongBiFunction< Localizable, T > idFromIntervalIndexer( fi
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* generalization for higher dimenions over a binary mask. {@code mask} and
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* {@code labeling} are expected to have equal min and max.
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*
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* @implNote op name='connectedComponents', type='org.scijava.function.Computers.Arity1'
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* @param mask
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* Boolean mask to distinguish foreground ({@code true}) from
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* background ({@code false}).
@@ -170,6 +171,44 @@ public static < B extends BooleanType< B >, L extends IntegerType< L > > void co
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new StartAtOneIdForNextSet() );
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}
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/**
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*
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* Implementation of connected component analysis that uses
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* {@link IntArrayRankedUnionFind} to find sets of pixels that are connected
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* with respect to a neighborhood ({@code shape}) over a binary mask.
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* {@code mask}
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* and {@code labeling} are expected to have equal min and max.
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* <p>
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* This method differs from
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* {@link #connectedComponents(RandomAccessibleInterval, RandomAccessibleInterval, Shape)}
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* only in that its parameter order is tailored to an Op. The output comes
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* last, and the primary input (the input image) comes first.
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* </p>
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*
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* @implNote op name='connectedComponents', type='org.scijava.function.Computers.Arity2'
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* @param mask
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* Boolean mask to distinguish foreground ({@code true}) from
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* background ({@code false}).
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* @param shape
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* Connectivity of connected components, e.g. 4-neighborhood
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* ({@link DiamondShape}), 8-neighborhood
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* ({@link RectangleNeighborhood}) and their generalisations for
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* higher dimensions.
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* @param labeling
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* Output parameter to store labeling: background pixels are
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* labeled zero, foreground pixels are greater than zero: 1, 2,
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* ..., N. Note that initially all pixels are expected to be zero
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* as background values will not be written.
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*/
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public static < B extends BooleanType< B >, L extends IntegerType< L > > void connectedComponents(
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final RandomAccessibleInterval< B > mask,
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final Shape shape,
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final RandomAccessibleInterval< L > labeling)
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{
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connectedComponents(mask, labeling, shape);
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}
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/**
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*
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* Implementation of connected component analysis that uses
@@ -216,6 +255,55 @@ public static < B extends BooleanType< B >, L extends IntegerType< L > > void co
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UnionFind.relabel( mask, labeling, uf, idForPixel, idForSet );
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}
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/**
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*
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* Implementation of connected component analysis that uses
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* {@link UnionFind} to find sets of pixels that are connected with respect
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* to a neighborhood ({@code shape}) over a binary mask. {@code mask} and
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* {@code labeling} are expected to have equal min and max.
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* <p>
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* This method differs from
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* {@link #connectedComponents(RandomAccessibleInterval, RandomAccessibleInterval, Shape, LongFunction, ToLongBiFunction, LongUnaryOperator)}
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* only in that its parameter order is tailored to an Op. The output comes
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* last, and the primary input (the input image) comes first.
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* </p>
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*
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* @implNote op name='connectedComponents', type='org.scijava.function.Computers.Arity5'
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* @param mask
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* Boolean mask to distinguish foreground ({@code true}) from
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* background ({@code false}).
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* @param shape
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* Connectivity of connected components, e.g. 4-neighborhood
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* ({@link DiamondShape}), 8-neighborhood
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* ({@link RectangleNeighborhood}) and their generalisations for
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* higher dimensions.
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* @param unionFindFactory
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* Creates appropriate {@link UnionFind} data structure for size
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* of {@code labeling}, e.g. {@link IntArrayRankedUnionFind} of
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* appropriate size.
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* @param idForPixel
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* Create id from pixel location and value. Multiple calls with
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* the same argument should always return the same result.
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* @param idForSet
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* Create id for a set from the root id of a set. Multiple calls
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* with the same argument should always return the same result.
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* @param labeling
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* Output parameter to store labeling: background pixels are
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* labeled zero, foreground pixels are greater than zero: 1, 2,
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* ..., N. Note that this is expected to be zero as background
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* values will not be written.
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*/
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public static < B extends BooleanType< B >, L extends IntegerType< L > > void connectedComponents(
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final RandomAccessibleInterval< B > mask,
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final Shape shape,
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final LongFunction< UnionFind > unionFindFactory,
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final ToLongBiFunction< Localizable, L > idForPixel,
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final LongUnaryOperator idForSet,
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final RandomAccessibleInterval< L > labeling)
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{
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connectedComponents( mask, labeling, shape, unionFindFactory, idForPixel, idForSet );
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}
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private static < B extends BooleanType< B >, L extends IntegerType< L > > UnionFind makeUnion(
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final RandomAccessibleInterval< B > mask,
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final RandomAccessibleInterval< L > labeling,

‎src/main/java/net/imglib2/algorithm/labeling/ConnectedComponents.java

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@@ -112,6 +112,41 @@ public static < T extends IntegerType< T >, L, I extends IntegerType< I > > void
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service.shutdown();
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}
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/**
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* Label all connected components in the given input image. In the output
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* image, all background pixels will be labeled to {} and foreground
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* components labeled as {1}, {2}, {3}, etc. where 1, 2, 3 are labels
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* returned by {@code labelGenerator.next()}. {@code labelGenerator.next()}
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* is called exactly <em>n</em> times if the input contains
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* <em>n</em> connected components.
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* <p>
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* This method differs from
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* {@link #labelAllConnectedComponents(RandomAccessible, ImgLabeling, Iterator, StructuringElement)}
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* only in that its parameter order is tailored to an Op. The output comes
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* last, and the primary input (the input image) comes first.
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* </p>
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*
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* @implNote op name='labelAllConnectedComponents', type='org.scijava.function.Computers.Arity3'
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* @param input
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* input image with pixels != 0 belonging to foreground.
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* @param labelGenerator
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* produces labels for the connected components.
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* @param se
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* structuring element to use. 8-connected or 4-connected
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* (respectively n-dimensional analog)
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* @param labeling
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* output labeling in which the connected components will be
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* labeled.
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*/
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public static < T extends IntegerType< T >, L, I extends IntegerType< I > > void labelAllConnectedComponents(
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final RandomAccessible< T > input,
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final Iterator< L > labelGenerator,
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final StructuringElement se,
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final ImgLabeling< L, I > labeling)
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{
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labelAllConnectedComponents( input, labeling, labelGenerator, se );
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}
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/**
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* Label all connected components in the given input image. In the output
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* image, all background pixels will be labeled to {} and foreground
@@ -154,6 +189,44 @@ public static < T extends IntegerType< T >, L, I extends IntegerType< I > > void
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labeling.getMapping().setLabelSets( labelSets );
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}
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/**
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* Label all connected components in the given input image. In the output
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* image, all background pixels will be labeled to {} and foreground
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* components labeled as {1}, {2}, {3}, etc. where 1, 2, 3 are labels
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* returned by {@code labelGenerator.next()}. {@code labelGenerator.next()}
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* is called exactly <em>n</em> times if the input contains
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* <em>n</em> connected components.
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* <p>
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* This method differs from
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* {@link #labelAllConnectedComponents(RandomAccessible, ImgLabeling, Iterator, StructuringElement, ExecutorService)}
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* only in that its parameter order is tailored to an Op. The output comes
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* last, and the primary input (the input image) comes first.
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* </p>
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*
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* @implNote op name='labelAllConnectedComponents', type='org.scijava.function.Computers.Arity4'
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* @param input
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* input image with pixels != 0 belonging to foreground.
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* @param labelGenerator
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* produces labels for the connected components.
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* @param se
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* structuring element to use. 8-connected or 4-connected
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* (respectively n-dimensional analog)
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* @param service
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* service providing threads for multi-threading
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* @param labeling
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* output labeling in which the connected components will be
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* labeled.
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*/
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public static < T extends IntegerType< T >, L, I extends IntegerType< I > > void labelAllConnectedComponents(
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final RandomAccessible< T > input,
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final Iterator< L > labelGenerator,
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final StructuringElement se,
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final ExecutorService service,
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final ImgLabeling< L, I > labeling)
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{
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labelAllConnectedComponents( input, labeling, labelGenerator, se, service );
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}
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/**
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* "Label" all connected components in the given input image. In the output
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* image, all background pixels will be set to 0 and foreground components

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