Challenges with Disk Arrays

Oct 13, 2025 by wbrum.org 53 views

Introduction

Image morphology operations, such as erosion and dilation, are essential in image processing and analysis. However, when dealing with large images stored on disk, these operations can be computationally expensive and time-consuming. In this article, we will explore the challenges of optimizing image morphology operations for disk arrays and provide a solution using a hack.

Background

Image morphology operations involve applying a structuring element (SE) to an image to transform it into a new image. The SE is a small image that is used to scan the original image and perform the transformation. Erosion and dilation are two common morphology operations that are used to reduce or increase the size of objects in an image.

Challenges with Disk Arrays

Disk arrays, such as Zarr arrays, are a type of data storage that is optimized for large datasets. However, when performing image morphology operations on disk arrays, there are several challenges that need to be addressed:

Indexing: Disk arrays use a different indexing scheme than in-memory arrays, which can make it difficult to access and manipulate the data.
Chunking: Disk arrays are typically stored in chunks, which can make it difficult to perform operations that require accessing large contiguous blocks of data.
Branching: The logic in the select function has too many branches, which can make it difficult to optimize the code.

The Hack

To address the challenges mentioned above, we can use a hack to optimize the image morphology operations for disk arrays. The hack involves rewriting the erode! and dilate! functions to use a different indexing scheme and to perform the operations in chunks.

Here is the code for the hack:

using ImageMorphology

for (fun, filt) in (("erode!", typemax), ("dilate!", typemin))
    fun_sym = Symbol(fun)
    @eval ImageMorphology.$fun_sym(out, img; dims=coords_spatial(img), r=nothing, chunk) =
        ImageMorphology.$fun_sym(out, img, strel_box(img, dims; r), chunk=chunk)

    @eval @doc """
        $($fun)(out, img, se; chunk)
    
    $($fun) `img` in chunks.  Doing so can be much faster than the generic
    element-wise algorithm if `img` is backed by, for example, a Zarr array.
    `chunk` should be a tuple with an element for each dimension.  The chunk
    can nominally be of any size but generally should be larger than `se` and
    the underlying chunk size of `img`.

    # Examples

    $($fun)(out, img, se; chunk=(64,64,64))
    """ ImageMorphology.$fun_sym
    @eval function ImageMorphology.$fun_sym(out, img, se; chunk)
        pad = extrema.(axes(se))
        PAD1 = CartesianIndex(ntuple(i->pad[i][1], length(pad)))
        PAD2 = CartesianIndex(ntuple(i->pad[i][2], length(pad)))
        ZERO = CartesianIndex(ntuple(_->0, ndims(img)))
        ONE = CartesianIndex(ntuple(_->1, ndims(img)))
        SIZEIMG = CartesianIndex(size(img))
        CHUNK = CartesianIndex(chunk)
        chunk_pad = [c+length(range(p...))-1 for (c,p) in zip(chunk,pad)]
        img_chunk = Array{eltype(img)}(undef, chunk_pad...)
        out_chunk = similar(img_chunk)
        for I in CartesianIndices((:).(ntuple(_->1, ndims(img)), chunk, size(img)))
            img_chunk .= $filt(eltype(img))
            R = min(SIZEIMG, I+CHUNK-ONE)
            IMG1 = max(ONE, I+PAD1)
            IMG2 = min(SIZEIMG, R+PAD2)
            img_chunk[ONE:IMG2-IMG1+ONE] .= img[IMG1:IMG2]
            ImageMorphology.$fun_sym(out_chunk, img_chunk, se)
            OUT1 = ONE-PAD1 + min(ZERO, I+PAD1-ONE)
            OUT2 = OUT1+R-I
            out[I:R] .= out_chunk[OUT1:OUT2]
        end
    end
end

Conclusion

In this article, we have explored the challenges of optimizing image morphology operations for disk arrays and provided a solution using a hack. The hack involves rewriting the erode! and dilate! functions to use a different indexing scheme and to perform the operations in chunks. This solution can be much faster than the generic element-wise algorithm if the image is backed by a Zarr array.

Future Work

There are several areas where this work can be improved:

Optimizing the select function: The select function has too many branches, which can make it difficult to optimize the code. We can try to optimize this function to reduce the number of branches.
Using a more efficient indexing scheme: The current indexing scheme used in the hack is not the most efficient. We can try to use a more efficient indexing scheme to improve the performance of the code.
Parallelizing the operations: We can try to parallelize the operations to take advantage of multiple CPU cores and improve the performance of the code.

Q: What are the challenges of optimizing image morphology operations for disk arrays?

A: The challenges of optimizing image morphology operations for disk arrays include indexing, chunking, and branching. Disk arrays use a different indexing scheme than in-memory arrays, which can make it difficult to access and manipulate the data. Additionally, disk arrays are typically stored in chunks, which can make it difficult to perform operations that require accessing large contiguous blocks of data. Finally, the logic in the select function has too many branches, which can make it difficult to optimize the code.

Q: What is the hack that you used to optimize the image morphology operations for disk arrays?

A: The hack that we used to optimize the image morphology operations for disk arrays involves rewriting the erode! and dilate! functions to use a different indexing scheme and to perform the operations in chunks. This solution can be much faster than the generic element-wise algorithm if the image is backed by a Zarr array.

Q: How does the hack work?

A: The hack works by rewriting the erode! and dilate! functions to use a different indexing scheme and to perform the operations in chunks. The hack involves the following steps:

Defining the chunk size: The chunk size is defined as a tuple with an element for each dimension.
Creating the chunk array: The chunk array is created using the Array function and is initialized with the same type as the input image.
Performing the operation in chunks: The operation is performed in chunks by iterating over the chunk array and applying the erode! or dilate! function to each chunk.
Storing the result: The result of the operation is stored in the output array.

Q: What are the benefits of using the hack?

A: The benefits of using the hack include:

Improved performance: The hack can improve the performance of image morphology operations for disk arrays by reducing the number of operations and improving the efficiency of the indexing scheme.
Scalability: The hack can make image morphology operations more scalable by allowing them to be performed on large images stored on disk.
Flexibility: The hack can provide more flexibility in the choice of indexing scheme and chunk size, allowing users to optimize the performance of the code for their specific use case.

Q: What are the limitations of the hack?

A: The limitations of the hack include:

Complexity: The hack can be complex to implement and may require a good understanding of the indexing scheme and chunking used in disk arrays.
Performance overhead: The hack may introduce a performance overhead due to the additional indexing and chunking operations.
Limited applicability: The hack may not be applicable to all types of images and may require modifications to work with different types of images.

Q: How can the hack be improved?

A: The hack can be improved by:

Optimizing the indexing scheme: The indexing scheme used in the hack can be optimized to reduce the number of operations and improve the efficiency of the code.
Improving the chunking scheme: The chunking scheme used in the hack can be improved to reduce the number of chunks and improve the efficiency of the code.
Parallelizing the operations: The operations performed in the hack can be parallelized to take advantage of multiple CPU cores and improve the performance of the code.

By addressing these areas, the hack can be further improved to provide better performance, scalability, and flexibility for image morphology operations on disk arrays.