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12 March 2008 Seeing through the window: pre-fetching strategies for out-of-core image processing algorithms
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Scientific data files have been increasing in size during the past decades. In the medical field, for instance, magnetic resonance imaging and computer aided tomography can yield image volumes of several gigabytes. While secondary storage (hard disks) increases in capacity and its cost per megabyte slumps over the years, primary memory (RAM) can still be a bottleneck in the processing of huge amounts of data. This represents a problem for image processing algorithms, which often need to keep in memory the original image and a copy of it to store the results. Operating systems optimize memory usage with memory paging and enhanced I/O operations. Although image processing algorithms usually work on neighbouring areas of a pixel, they follow pre-determined paths through the image and might not benefit from the memory paging strategies offered by the operating system, which are general purpose and unidimensional. Having the principles of locality and pre-determined traversal paths in mind, we developed an algorithm that uses multi-threaded pre-fetching of data to build a disk cache in memory. Using the concept of a window that slides over the data, we predict the next block of memory to be read according to the path followed by the algorithm and asynchronously pre-fetch such block before it is actually requested. While other out-of-core techniques reorganize the original file in order to optimize reading, we work directly on the original file. We demonstrate our approach in different applications, each with its own traversal strategy and sliding window structure.
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R. Pinho, K. J. Batenburg, and J. Sijbers "Seeing through the window: pre-fetching strategies for out-of-core image processing algorithms", Proc. SPIE 6919, Medical Imaging 2008: PACS and Imaging Informatics, 69190D (12 March 2008);

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