Open source software and Interdisciplinary data management: Post-surgery rehabilitation case study. Presented by Boris Bačić, AUT University, at HINZ 2014, 12 November 2014, 12.22pm, Plenary Room 2

1. Open Source Software and
Interdisciplinary Data Management:
Post-surgery Rehabilitation Case Study
Boris Bačić1, Sayumi Iwamoto2 and Dave Parry1
1Auckland University of Technology, School of Computer and Mathematical Sciences
Private Bag92006, Auckland 1142, New Zealand
{boris.bacic|dave.parry}@aut.ac.nz
2Toyo University, Department of Health Care and Sports
48-1, Oka, Asaka-shi,Saitama 351-8510, Japan
siwamoto@toyo.jp

2. Motivation
Aim
• To help a young athlete during the last
stage of her post-surgery rehabilitation.
• To validate, reconsider or adapt the:
1. Biomechanics of:
Motion patterns, ..., and Style
2. Sport equipment
3. Analysis, Feedback/Intervention in
collaboration with medical
specialists.
• To address the need for technology to
support the post-surgery rehabilitation &
related activities (Knudson & Morrison, 2002, p. 80)
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3. Motivation
Requirements for a
specialist support team
– A team of specialists to
provide multi-disciplinary
expertise and a
combination of efforts
– A team set up in an
ad-hoc fashion without a
pre-established means of
communicating or sharing
data.
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4. Problem Statement / Technology Aspects
Questions:
• Can we utilise open-source
software (OSS) tools to
support the last stage of
rehabilitation?
• Can the OSS for the identified
tasks be modified to support
related areas (e.g. ageing
populations, well-being
rehabilitation, sport science
and coaching)?
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5. Challenges
• The challenges include:
– Privacy during patient data exchange
– Clinical and technical requirements
– Costs: In NZ tennis is a "non-carded" sport i.e. not financially
supported (unlike e.g. rugby, netball or cricket). However, the
first author (who initialised the ad-hoc team collaboration)
was approached for help from an HPSNZ and SPRINZ
associate
– The need for data exchange and management, taking into
account the efficiency of multi-device, multi-platform and
multi-software integration, and task automation
– The use of diverse systems. Multi-disciplinary team
preferences and information system requirements are nearly
impossible to anticipate
– Selecting augmented coaching technology to support
coaching and rehabilitation activities.
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6. The Study
1. Post-surgery rehabilitation case study background
– Return-to-sport phase approx. one year after her shoulder
surgery. AUT Ethics approval: AUTEC # 12-18
– Modifying targeted movement patterns to increase safety,
comfort and to address the 'fear of re-injury'
– Technology and privacy aspects.
2. Decision
• To use Open-Source Software (OSS) and generic hardware
that can support complex ad-hoc specialist collaborations and
augmented coaching without:
– Requiring professionals to share various software packages
– Using proprietary (or non-common) data formats and tools.
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7. Case Study Background
Participants
• An elite-level junior tennis player who had already represented the country
in competing locally and internationally. Approximately one year after the
shoulder surgery, she was still unable to serve without pain.
• An ad-hoc team who combined their efforts and expertise.
Applications of technology
• To assist with modifying and personalising the biomechanics of the athlete’s
serve, overall technique and training
• To support the tasks of collecting and annotating a large collection of data
files including: radiology imaging, high-speed/regular-speed videos of the
athlete’s movement, photos, voice notes and various other documents
• To allow the efficient use of bandwidth, storage space and other
computational resources for moving and consolidating files between diverse
systems
• To support multi-platform viewing and editing for the international team
and athlete to consult effectively, and to develop and follow-up on the
rehabilitation plan. 7

8. Case Study Specifics
Specialist coaching-related activities
• Learning the athlete's medical history and rehabilitation progress
• Working with the athlete (and her support group)
• Considering sport equipment changes
• Establishing a multi-disciplinary ad-hoc collaboration
• Planning and preparing a training plan, capturing data, producing an
analysis, and then proposing changes and how to implement them
• Validating the change of the athlete's serve biomechanics with
medical professionals/specialists
• Choosing augmented coaching technology for coaching support
(Bačić & Hume, 2012)
• Securing data (data exchange, synchronisation, encryption,
consolidation, backup and retrieval).
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9. Methodology Aspects
The case study research:
• Has a cyclic and qualitative nature
• Is taking into account multi-disciplinary team
preferences and information system requirements
• Produced user scenarios that were used in the
selection and adaptation of Linux-based OSS tools.
The use of user scenarios helped to identify tasks,
elicit requirements and challenges for people
interacting with technology.
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10. Solution
• The Linux-based OSS tools used included:
Ubuntu 12.04 LTS, cp, rsync, zip/unzip,
ImageMagick’s mogrify, and ffmpeg.
• Data duplication
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11. Achieved Solutions and Results
User scenarios, associated tasks and functionality
requirements ...
Windows Mac OS-X Linux
Function and Command Utility (XP, 7 and 8)
(ver 10.6 or
higher)
Ubuntu 12.04 or
higher
Briefcase concept file transfer xcopy rsynch cp -u
Compression and Decryption zip zip zip
Encryption Used EFS zip -e zip -e
Batch image processing for video
slide show
ImageMagic /
mogrify
Video segments extraction
(or voice notes e.g. mp3) ffmpeg
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12. Running Radiology Software
Windows-based Radiology Software Running on Linux
Wine configuration example:
wine ~/CODONICSnnnnnn/bin/Virtua.exe
where the text / CODONICSnnnnnn/represents installation directory that may be found and copied from
the original radiology installation CD.
Note: The X-ray image areas were darkened with suboptimal contrast setting to deliberately hide details and
demonstrate ad-hoc and optimal interactive viewing of region of interest 12 by using mouse control in Ubuntu.

13. Technology Trends:
USB/SD Capture and Tablet Replay
FILE TRANSFER Add-hoc based Video Replay or Image Slide Show
Coaching…
Recommended Steps :
1. Record media files: video or a set of time-lapsed photos
2. Convert media files to target resolution for a tablet
3. Transfer video file(s) via e.g. SD adaptor/USB cable to a laptop or a tablet
4. Delete original files on SD (optional and convenient for continuing
coaching…)
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14. Results: Personalised Gym Programme
Slide Show
Batch Image Processing/Resizing Results:
HDD: 2TB, 7200 rpm.
• Directory containing original photos showing gym
programme demonstration:
3,024 images (with total size of 12.7 GB)
• Time to copy the directory with the original images
(3000 x 2250):
3 min and 34 sec
• Time to resize and rewrite (overwrite) all images:
9 min and 45 sec.
Resolution and size reduction:
3000x2250 into 1200x768 12.7 GB pixels
12.7 GB into 1.8 GB
• Command to resize and rewrite all images:
mogrify
Note:
Time to copy resized (1024x720 pixels) images: 2 sec.
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15. Results: High-speed Video
A-B Sequence Extraction and Copy
Relative comparisons of processing results for shorter and longer video segments
Extraction and copy command: ffmpeg
- No transcoding or recompression of video or audio information
Original high-speed video file properties
Video file size: 3.2 GB (3,160,837,169 bytes)
Duration: 13 min 52 sec
Dimensions: 1280 x 720
Codec: H.264 / AVC
Frame rate: 120 frames per second
Bit rate: 30235 kbps
Audio
Codec: MPEG-4 AAC
Bit rate: 128 kbps
Sample rate: 48000 Hz
Video Short Sequence Long Sequence
Duration 0 min 2.233 sec 6 min 0 sec
Extracted File Size 435.9 MB 1.4 GB
Copy 0 min 2.233 sec 0 min 7.561 sec
Extract and Copy 0 min 2.942 sec 0 min 9.385 sec
Note: The achieved performance of ffmpeg command with its parameter configuration that allows extraction
of video sequence without quality loss shows similar performance of file copy command cp.
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16. Discussion
Generic concerns for data safety, patient's privacy and backup
• File encryption and data storing
– Linux distributions allow encryption of a user account data
– Open-source software and third party tools
– Risk of data exposure during short-term (or temporary) data
processing or physical transfer (e.g. via USB stick or other media).
• Data storage options
– Encrypted HDD enclosure
– Network Attached Storage (NAS), Personalised Cloud ...
– Cloud services (NZ and outside of our national jurisdiction) ,
"reasonable care" agreement clause ...
• Alternative software:
– Windows: IrfanViewer, VirtualDub (with codec plug-ins), Handbrake,
– Linux: ffmpeg, mencoder, aviconv .
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17. Conclusion
• The rehabilitation was successful and the athlete after returning-to-sport
(six month programme), successfully qualified for a US
University and tennis programme scholarship.
• This study showed that OSS tools can effectively be used to support
sports rehabilitation in a complex and heterogeneous computing
environment. Such approaches may be useful for other complex ad-hoc
collaborations, without requiring professionals to share various
software packages or non-common data format tools.
• The augmented video coaching technology and open-source tools
can be extended to related areas e.g. sport science, coaching,
physiotherapy, rehabilitation and assisting aging population to
regain mobility, stability and movement control.
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18. Future Work
• Need to repeat similar case studies
• Technology and preliminary experiments
– Embedded Linux for personalised encrypted storage/
cloud
– OS Platform virtualisation for remote processing tasks
– Client/Server text-to-graphics remote display/score
board. Wired and wireless solutions.
– Mobile/tablet multi-user distributed video acquisition
and editing – web and cloud service oriented integrative
approaches
– Low-cost embedded sensors, video and 3D data real-time
acquisition, streaming and integration.
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19. Questions?
Acknowledgements
• Dr. Matthew Brick and Acupuncturist Xiaodong (Dong) Shen for help with their
medical insights, astute observations and shown collaborative efforts.
• Ariel McGrigor (Auckland Radiology Group) for his help in obtaining patient's
medical history and recording digitised records to off-line storage.
• Kevin Woolcott for sharing his views pertinent to the study, coaching technology
and tennis equipment.
• Millennium gymnasium for four weekends free access.
References
Knudson, D. V., & Morrison, C. S. (2002). Qualitative analysis of human movement (2nd
ed.). Champaign, IL: Human Kinetics.
Bačić, B., & Hume, P. (2012, 2-6 Jul). Augmented video coaching, qualitative analysis
and post-production using open source software. Australian Catholic University
(ACU) Melbourne. Symposium conducted at the meeting of the XXX International
Symposium on Biomechanics in Sports (ISBS), Melbourne, Australia.
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20. Recap
• Return-to-sport rehabilitation stage
– The last stage of post-surgery rehabilitation is return-to-sport
– The aim of return-to-sport for high-performance athletes is to allow them to return
to their sport and to continue competing
– Need to adapt: motion patterns, technology and work with medical specialists.
– a. • Requirements for specialist support team
– Need for a multi-disciplinary specialist support team
– Team support set up in an ad-hoc fashion without pre-established
means of communication or data sharing.
• Need for supporting technology
– Augmented coaching technology and its integration
– Technology to communicate, share, process, consolidate,
encrypt, backup and retrieve data.
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