Insight Journal - Performance Benchmarking the Insight Toolkit

Performance Benchmarking the Insight Toolkit

Please use this identifier to cite or link to this publication: http://hdl.handle.net/10380/3557

Published in The Insight Journal - 2016 January-December.

Submitted by Matthew Mccormick on 07-01-2016.

This document describes a module for the Insight Toolkit (ITK) to assist in performance
benchmarking and a suite of benchmarks for the toolkit. These resources provide metrics to quantify
software computational performance. This is a pre-requisite to improve performance either through
algorithmic advancements or better utilization of hardware resources.
Computational performance is quantified by reducing factors that confound timing measurements and
by estimating measurement variance. New classes are presented that increase operating system process
priority to minimize the impact of other processes running on the system. System hardware characteristics
are extracted and displayed. The influence of hard disk input/output on runtime measurements is
removed in the suite of benchmarks. Additionally, the number of threads used by each benchmark can be
specified. These benchmarks consist of common analysis pipelines and run on 3D magnetic resonance
brain image data so realistic performance is quantified. Benchmarks can be executed with multiple iterations,
and timing statistics are recorded in tab separated value (.tsv) files, which are easily stored or
processed for further analysis and visualization.
This paper is accompanied with the source code, input data, parameters and output data that the authors
used for validating the algorithm described in this paper. This adheres to the fundamental principle
that scientific publications must facilitate reproducibility of the reported results.

Data

1 Dataset (5Mb)

brainweb165a10f17.mha (5Mb)

Code

There is no code review at this time.

Reviews

There is no review at this time. Be the first to review this publication!

Quick Comments

Comment by Altheqa Stone

https://www.altheqa-eg.com/stone-prices/
https://www.dekorishn-altheqa.com/decoration/
https://www.altheqa-eg.com/stone-types/
https://www.altheqa-stone.com/hashmi-stone-prices/
https://www.decoration-altheqa.com/stone-facades/
https://www.altheqa-stone.com/stone-2020/
https://www.dekorishn-altheqa.com/modern-stone-2/
https://www.dekorishn-altheqa.com/stone-houses/
https://www.altheqa-stone.com/altheqa-stone/
https://www.altheqa-eg.com/black-basalt/
https://www.decoration-altheqa.com/basalt-altheqa/
https://www.altheqa-eg.com/%D8%AA%D8%B1%D9%83%D9%8A%D8%A8-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D9%87%D9%8A%D8%B5%D9%85-%D8%AE%D8%B7%D9%88%D8%A9-%D8%A8%D8%AE%D8%B7%D9%88%D8%A9/
https://www.altheqa-eg.com
https://www.altheqa-eg.com/%d8%a3%d9%87%d9%85-%d8%a7%d9%84%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d9%84%d9%88%d8%b8%d9%8a%d9%81%d8%a9-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5/
https://www.altheqa-eg.com/%d9%85%d8%b9%d8%b1%d9%81%d8%a9-%d8%a3%d8%b3%d8%b9%d8%a7%d8%b1-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d9%81%d9%8a-%d9%85%d8%b5%d8%b1/
https://www.altheqa-eg.com/%d9%85%d8%b9%d8%b1%d9%81%d8%a9-%d8%a3%d8%b3%d8%b9%d8%a7%d8%b1-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d9%81%d9%8a-%d9%85%d8%b5%d8%b1/
https://www.altheqa-eg.com/%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/
https://www.altheqa-stone.com/stone-decorations/
https://www.altheqa-stone.com/%d8%aa%d8%b9%d8%b1%d9%81-%d8%b9%d9%84%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/export/
https://www.altheqa-stone.com/%d8%aa%d8%b9%d8%b1%d9%81-%d8%b9%d9%84%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/%d8%b3%d8%b9%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%88%d8%b7%d8%b1%d9%8a%d9%82%d9%87-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8%d8%a9/
https://www.altheqa-stone.com/%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%D9%84%D9%85%D8%A7%D8%B0%D8%A7-%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D8%AA%D9%83%D9%84%D9%81-%D8%A7%D9%85%D9%88%D8%A7%D9%84-%D9%83%D8%AB%D9%8A%D8%B1/
https://www.altheqa-stone.com/
https://www.altheqa-stone.com/category/hism-stone/exterior-decorations/
https://www.altheqa-stone.com/stone/
https://www.altheqa-stone.com/stone-altheqa/
https://www.altheqa-stone.com/hism-stone/
https://www.altheqa-stone.com/stone-2/
https://www.altheqa-stone.com/stone-3/
https://www.altheqa-stone.com/stone-decorations/
https://www.altheqa-stone.com/%d9%83%d9%84-%d9%85%d8%a7-%d9%87%d9%88-%d8%ac%d8%af%d9%8a%d8%af-%d9%81%d9%89-%d8%b9%d8%a7%d9%84%d9%85-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d8%b4%d9%83%d8%a7%d9%84-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%aa%d8%b9%d8%b1%d9%81-%d8%b9%d9%84%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/%d8%a7%d9%81%d8%b6%d9%84-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%b9%d9%85%d8%a7%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d9%81%d8%b6%d9%84-%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d8%aa%d8%b5%d9%85%d9%8a%d9%85%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%b3%d9%88%d9%81-%d8%aa%d9%86%d8%a7%d9%84-%d8%a7%d8%b9%d8%ac%d8%a7%d8%a8%d9%83/
https://www.altheqa-stone.com/%d9%85%d9%87%d9%86%d8%af%d8%b3%d9%8a%d9%86-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/export/
https://www.altheqa-stone.com/stone-altheqa/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d9%88%d9%85%d9%86%d8%a7%d8%b2%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%85%d9%85%d9%8a%d8%b2%d8%a7%d8%aa-%d9%88%d8%b9%d9%8a%d9%88%d8%a8-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d8%b3%d8%b9%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%88%d8%b7%d8%b1%d9%8a%d9%82%d9%87-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8%d8%a9/
https://www.altheqa-stone.com/%d8%b4%d8%a7%d9%87%d8%af-%d8%a7%d8%ad%d8%af%d8%ab-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d8%a7%d8%a8%d8%aa%d9%83%d8%a7%d8%b1-%d9%81%d9%89-%d8%a7%d9%84%d8%aa%d8%b5%d9%85%d9%8a%d9%85-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%85%d9%86%d8%a7%d8%b2%d9%84-%d8%ae%d8%a7%d8%b1%d8%ac%d9%8a%d8%a9/
https://www.altheqa-stone.com/%d8%b4%d8%b1%d9%83%d8%a9-%d8%aa%d8%b5%d8%af%d9%8a%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-stone.com/%d9%85%d9%82%d8%a7%d9%88%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-stone.com/category/hachmi-stone-facades/
https://www.altheqa-stone.com/category/hism-stone/
https://www.altheqa-stone.com/%d8%aa%d8%b5%d9%85%d9%8a%d9%85%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%b3%d9%88%d9%81-%d8%aa%d9%86%d8%a7%d9%84-%d8%a7%d8%b9%d8%ac%d8%a7%d8%a8%d9%83/
https://www.altheqa-stone.com/%d8%a7%d9%81%d8%b6%d9%84-%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%89-%d9%81%d9%89-%d9%85%d8%b5%d8%b1/
https://www.altheqa-stone.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%85%d9%86%d8%a7%d8%b2%d9%84-%d9%88%d9%81%d9%84%d9%84-%d9%81%d8%a7%d8%ae%d8%b1%d8%a9-%d8%a8%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85/
https://www.altheqa-eg.com
https://www.altheqa-eg.com/category/hachemi-stone/
https://www.altheqa-eg.com/%d8%aa%d9%86%d9%81%d9%8a%d8%b0-%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d8%a3%d9%87%d9%85-%d8%a7%d9%84%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d9%84%d9%88%d8%b8%d9%8a%d9%81%d8%a9-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5/
https://www.altheqa-eg.com/%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ae%d8%a7%d8%b1%d8%ac%d9%8a%d8%a9-%d8%a7%d9%81%d8%b6%d9%84-%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d9%88%d9%85%d9%86%d8%a7%d8%b2%d9%84/
https://www.altheqa-eg.com/%d9%85%d8%b9%d8%b1%d9%81%d8%a9-%d8%a3%d8%b3%d8%b9%d8%a7%d8%b1-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d9%81%d9%8a-%d9%85%d8%b5%d8%b1/
https://www.altheqa-eg.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a8%d8%a7%d9%84%d8%b5%d9%88%d8%b1-%d9%88%d8%a7%d9%84%d9%81%d8%af%d9%8a%d9%88%d9%87%d8%a7/
https://www.altheqa-eg.com/%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d9%87%d9%88-%d8%a7%d9%84%d8%a7%d9%81%d8%b6%d9%84-%d8%af%d8%a7%d8%a6%d9%85%d8%a7-%d9%84%d9%85%d8%a7%d8%b0%d8%a7%d8%9f/
https://www.altheqa-eg.com/category/stone/
https://www.altheqa-eg.com/%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85-%d8%ae%d8%b7%d9%88%d8%a9-%d8%a8%d8%ae%d8%b7%d9%88%d8%a9/
https://www.altheqa-eg.com/%d8%a7%d8%ad%d8%af%d8%ab-%d9%85%d9%82%d8%a7%d9%84%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ac%d8%b0%d8%a7%d8%a8%d9%87-%d9%85%d9%86-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a7%d8%b3%d8%b9%d8%a7%d8%b1-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5%d9%85/
https://www.altheqa-eg.com/%d8%a7%d8%b4%d9%83%d8%a7%d9%84-%d9%88%d8%a7%d9%86%d9%88%d8%a7%d8%b9-%d8%a7%d9%84%d8%ad%d8%ac%d8%b1-%d8%a7%d9%84%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d8%a7%d9%84%d9%85%d8%aa%d9%88%d8%a7%d8%ac%d8%af%d9%87/
https://www.altheqa-eg.com/%d8%a7%d8%b4%d9%8a%d8%a7%d8%a1-%d9%8a%d8%ac%d8%a8-%d8%a7%d9%86-%d8%aa%d9%81%d8%b9%d9%84%d9%87%d8%a7-%d9%81%d9%89-%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d8%aa%d8%b5%d9%85%d9%8a%d9%85-%d8%af%d9%8a%d9%83%d9%88%d8%b1%d8%a7%d8%aa-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/%d9%88%d8%a7%d8%ac%d9%87%d8%a7%d8%aa-%d9%81%d9%84%d9%84-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.altheqa-eg.com/stone-altheqa/
https://www.altheqa-eg.com/%d8%b4%d8%b1%d9%83%d8%a9-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89/
https://www.pinterest.com/altheqa_stone/%D8%AA%D8%B5%D9%85%D9%8A%D9%85-%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D9%85%D9%86%D8%A7%D8%B2%D9%84-%D9%88%D8%B9%D9%85%D8%A7%D8%B1%D8%A7%D8%AA-%D8%A8%D8%A7%D9%84%D8%AD%D8%AC%D8%B1-%D8%A7%D9%84%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D8%A8%D8%AA%D8%B5%D9%85%D9%8A%D9%85%D8%A7%D8%AA/
https://www.pinterest.com/decoration_altheqa/%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89/
https://www.facebook.com/alth8h/
https://www.pinterest.com/decoration_altheqa/home-design%D9%88%D8%A7%D8%AC%D9%87%D8%A7%D8%AA-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89-%D9%87%D9%8A%D8%B5%D9%85/
https://www.dekorishn-altheqa.com/%D8%A7%D8%B3%D8%B9%D8%A7%D8%B1-%D8%AD%D8%AC%D8%B1-%D9%87%D8%A7%D8%B4%D9%85%D9%89/

https://www.altheqa-eg.com/%d8%a3%d9%87%d9%85-%d8%a7%d9%84%d8%b4%d8%b1%d9%83%d8%a7%d8%aa-%d9%84%d9%88%d8%b8%d9%8a%d9%81%d8%a9-%d8%aa%d8%b1%d9%83%d9%8a%d8%a8-%d8%ad%d8%ac%d8%b1-%d9%87%d8%a7%d8%b4%d9%85%d9%89-%d9%87%d9%8a%d8%b5/

Resources


Download All
Download Paper , View Paper
Download Source code
Source code repository

Statistics more


Global rating:
Review rating:	[review]
Code rating:
Views:	11782
Downloads:	3009
Paper Quality:
1 comment

Information more


Paper Id:	972
Categories:	Code speed optimization, Parallelization, SMP, Programming
Keywords:	Performance, Benchmarking, Threading
Toolkits:	ITK, CMake
Revision:
Export citation:
Status:	Open for public review

Share

Linked Publications more


InsightToolkit Kinetic Analysis (itk::ka) Library by Dowson N., Baker C., Raffelt D., Smith J., Thomas P., Salvado O., Rose S.
OpenCL accelerated GPU binary morphology image filters for ITK by Bardosi Z.
Scalable Simple Linear Iterative Clustering (SSLIC) Using a Generic and Parallel Approach by Lowekamp B., Chen D., Yaniv Z., Yoo T.
Computing Bone Morphometric Feature Maps from 3-Dimensional Images by Vimort J., McCormick M., Paniagua B.
Efficient multithreading for manycore processor: Multidimensional domain decomposition using... by St-Onge E., Scherrer B., Warfield S.K.
Computing Textural Feature Maps for N-Dimensional images by Vimort J., McCormick M., Budin F., Paniagua B.
Anomalous Diffusion Paradigm for Image Denoising Process by Senra Filho A.C., Murta Junior L.O.
Perturbing Mesh Vertices with Additive Gaussian Noise by Vigneault D.
A new implementation of itk::ImageToImageFilter for efficient parallelization of image processing... by Jaberzadeh A., Scherrer B., Warfield S.
A patch-based framework for new ITK functionality: Joint fusion, denoising, and non-local... by Tustison N., Avants B., Wang H., Xie L., Coupe P., Yushkevich P., Manjon J.

View license

Loading license...

Send a message to the author