Block algorithms: type conversion and downsampling #97
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…ting between pixel types The new package net.imglib2.algorithm.blocks contains algorithms that operate on primitive arrays using the PrimitiveBlocks utility added in imglib2 6.2.0. The net.imglib2.algorithm.blocks root and .util packages contain helpers to define and chain block operators and to use them for creating CellImgs. The net.imglib2.algorithm.blocks.convert package contains a type conversion operator to convert between (primitive arrays corresponding to) standard ImgLib2 RealTypes.
The net.imglib2.algorithm.blocks.downsample package provides operators for downsampling blocks of (primitive arrays corresponding to) standard ImgLib2 RealTypes. Downsampling is always factor of 2 (in one ore more dimensions). There are versions for downsampling 2x2x2... blocks with half-pixel offset and 3x3x3... blocks on pixel centers.
tpietzsch
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This PR provides
PrimitiveBlocksutility introduced in imglib2 6.2.0.Package
net.imglib2.algorithm.blockcontains helpers to define and chain block operators.In particular, the
BlockProcessor<I,O>interface specifies an algorithm that computes values in a flattened primitive output array (typeO) from values in a flattened primitive input array (typeI).To avoid mistakes in unchecked casting of primitive array types,
BlockProcessorshould be typically wrapped inUnaryBlockOperator<S,T>whereSandTare source and target ImgLib2 RealType corresponding to the respectiveIandOarray types.UnaryBlockOperatorcan be chained usingUnaryBlockOperator.andThen(...).Block algorithms are intended to run single-threaded.
Multi-threading is achieved on a coarser level by using them in
CellLoadersforCahcedCellImgand creating multiple cells in parallel.An operator to convert between common
RealTypes (signed and unsigned, with and without clamping).This code is partially auto-generated using the
bin/generate.groovyscript lifted from scijava-ops.An operator to downsample, by factor 2, blocks of common
RealType.It can be specified whether intermediate calculations should happen in FLOAT or DOUBLE precision (or AUTOmatically determined). There are versions for downsampling 2x2x2... blocks with half-pixel offset and 3x3x3... blocks on pixel centers.
Together with
PrimitiveBlocksfrom imglib2 core, the downsampling algorithm achieves speedup offactor ~4 over the downsampling used in bigdataviewer-core, and speedup of factor ~10 to ~30 over the downsampling used in BigStitcher (depending on Java version, block size, etc).
(This is on
ArrayImginputs. Speedups are probably even larger forCellImgorPlanarImginputs, wherePrimitveBlockshas a larger impact.)I will make PRs to BigStitcher and bigdataviewer-core when this is merged and released.