Industrial Training Report 1999-2000

Industrial Training Report by Bhautik Joshi (2210847)

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Industrial Training Report 1999-2000

Bhautik Joshi2210847

[email protected]


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Table of Contents

1.0 INTRODUCTION................................................................................................................................... 3

2.0 PROJECTS............................................................................................................................................ 4

2.1 Development of Tools for Aortic Aneurysm Visualisation ............................................................. 4

2.1.1 Overview..................................................................................................................................................4

2.1.2 Hardware & Software...............................................................................................................................4

2.1.3 Scientific Background ..............................................................................................................................5

2.1.4 Existing Work ..........................................................................................................................................7

2.1.5 Tools Developed ......................................................................................................................................7

2.1.6 Movies generated .....................................................................................................................................9

2.2 Investigation of the effects of attenuating materials on or near the feed horns of the ATCA ...... 12

2.2.1 Overview................................................................................................................................................12

2.2.2 Report.....................................................................................................................................................12

3.0 TRAINING ......................................................................................................................................... 12

4.0 RELEVANCE OF WORK EXPERIENCE TO STUDIES.............................................................................. 13

5.0 CONCLUSION.................................................................................................................................... 13


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1.0 Introduction

Over the summer of 1999 to 2000, one was granted the unique opportunity to be employed by the

division of Telecommunications and Industrial Physics within CSIRO as part of the Vacation Scholarship

program. Under the supervision of Laurie Wilson of at Image and Signal Processing, I was lucky enough

to undertake two exciting and rewarding projects that expanded my horizons and my way of thinking.

The Telecommunications and Industrial Physics (TIP) division in CSIRO is based in Sydney, at two sites;

namely its base at Marsfield and the National Measurement Laboratory at Lindfield. The Marsfield site is

shared with the Australia Telescope National Facility (ATNF) and the Anglo-Australian Observatory

(AAO). TIP deals with many varied aspects of Telecommunications and Physics, from antenna research

to research into Medical Imaging. The division developed products traditionally on a pure research basis;

however, now sells to a huge commercial market, with its cutting edge technology sold and used all over

all over the world.

My main project was based within the ‘Image and Signal Processing’ (ISP) discipline and primarily

involved developing a set of tools and for Medical Imaging visualisation, under the supervision of Laurie

Wilson of that discipline.

My secondary project was part of the Vacation Scholarship program. As part of the program, vacation

scholars at TIP join the other scholars from the ATCA and AAO in undertaking a series of experiments at

the Australia Telescope Compact Array (ATCA) radiotelescope at Narrabri. I led a small team in

designing and implementing a unique and peculiar engineering experiment at the ATCA.


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2.0 Projects

2.1 Development of Tools for Aortic Aneurysm Visualisation

2.1.1 OVERVIEW

CSIRO has a wide range of products and services available; its diversity in its research is hard to get a

clear picture on and to the public seems to be largely mysterious and enormous organisation. To better

deal with this, the CSIRO is opening a ‘Discovery Centre’ in Canberra later this year.

One of the primary goals of my work was to showcase one of the tools developed to visualise aortic

aneurysms based on CT data in a series of short videos (about two to three minutes in length). As part of

this, a set of visualisation tools were developed using a wide variety of software and hardware.

2.1.2 HARDWARE & SOFTWARE

The software was primarily developed on a well-configured Silicon Graphics Indigo 2 machine, with 128

Mb of memory, numerous mounted hard disks littered all over the local network. The machine was

running Irix 6.5 (a unix-like operating system) but easy access to machines and terminals running a

numerous variety of operating systems from unix to NT.

The project was developed under two main software platforms, namely a standard Java environment for

the Knowledge Based Segmentation, and a special visualisation package, AVS/Express for visualisation.

Both will be discussed in depth in later sections.


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2.1.3 SCIENTIFIC BACKGROUND

The Abdominal (or descending) Aorta is

the main blood supply for the thorax and

lower body, as shown in fig Figure 2-1.

Every time that blood is sent from the

heart down the aorta, the aorta pulsates

and expands to permit the blood to flow.

Over time, the aorta expands and

contracts many millions of times. This

frequent stress over time weakens the

walls of the aorta; sometimes this

weakening is so severe that the body

reacts by a swelling around the

weakened area known as an

‘Aortic Aneurysm’.

Figure 2-2 shows such a typical

aneurysm. The aorta is shown

with the thrombus as a semi-

transparent swelling around the

affected area. The danger to the

patient is that the weakened walls

are so badly affected that they

Figure 2-1 – Anatomical position of Abdominal Aorta

(source: ‘Mosbys Crash course: Anatomy’, Phillip

Ameerally, Mosby, 1998, p.73)

Figure 2-2 – Aortic Aneurysm

(derived from CT data)

Aorta

Thrombus

Iliac Arteries


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may well rupture, killing the patient in a number of hours.

This condition is corrected by surgery that inserts a ‘stent graft’ into the flow channel that reinforces the

walls of the aorta and reduces the swelling. However, it has been very difficult for surgeons to determine

the size and shape of the stent graft needed.

Previously, surgeons had to rely on looking at individual CT scans to determine the size and extent of the

aorta and the thrombus (see figure 2-3). This was time consuming and difficult to do, not always

producing accurate results.

Software developed at CSIRO takes these ‘slices’ of CT data and, using knowledge based segmentation

techniques, turns this segmented data into a three-dimensional model of an aorta (see figure 2-2). It was

the aim of the project to use this model to produce various visualisations of the aorta in such a way that

would be both informative and pleasing to the eye.

Figure 2-3 – Sequence of CT slices


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2.1.4 EXISTING WORK

A group of students last year developed a simple ‘fly through’ of the aorta. This served as an excellent

starting point for the project. However, the existing model had several flaws (see fig 2-4a & 2-4b);

namely that the old model had no colour, had rough aorta walls and did not show any calcification (solid

deposits on the aorta walls). The old model was also very hard to generate and took quite a while to

render.

2.1.5 TOOLS DEVELOPED

Two platforms were used for software development, namely Java and AVS/Express.

2.1.5.1 Java Development

The existing knowledge based segmentation software was written in Java. Very little development was

necessary in Java primarily because it was already written. Small amounts of code were written to

improve the way the brightness of the CT data was read so that a better map of the calcification could be

made, but, otherwise, the code remained untouched.

2.1.5.2 AVS/Express Development

AVS/Express is a ‘visual’ object oriented programming environment for visualising the data. Data is

processed through what is known as a ‘network’ of interconnected modules that link together to visualise

the data.

Figure 2-4a (left) & 2-4b (right) – old model & new model


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AVS tended to be hard to use, buggy, and temperamental. However, it was good for prototyping and very

simple to get up and running relatively quickly. The modules each have input and output ports;

corresponding ports are connected together to operate on the data.

AVS provides many pre-written modules that can be connected together to process incoming data.

However, these modules tend to be rather simple and lack functionality. To get around this, it is possible

for the user to write custom modules in C or C++ to process the data. My entire module writing work for

the project was in C as it did fit with the procedural nature of the project.

Figure 2-5 AVS/Express window and final network


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Figure 2-5 illustrates the top-level network used to create the final movies. Each module shown is

comprised of sub-networks, which either break down to normal AVS modules or C functions that are

compiled to run within AVS.

The important modules developed are shown on the network. At the top there are the ‘get CT’ modules.

Here, raw CT scan data is converted into a format that AVS can display. A C function was necessary to

preprocess the data into a cleaner format.

The ‘viz’ module is used to correctly scale and display the various static models, including the aorta, any

grids and the model of the human that is used (see later section). Here, no custom modules needed to be

written.

The ‘flightpath’ module is primarily user written code, and guides the camera down a ‘flight path’

through the aorta. A good deal of mathematics was involved here, and several techniques (which cannot

be entered into here for copyright reasons) were used to give the impression of a ‘smooth’ flight.

The final two modules, Uviewer3D and Image Capture were used to finally display the models and

capture them into a movie sequence.

Future scope for the project includes porting the AVS modules into Java and having the entire system run

under Java.

2.1.6 MOVIES GENERATED

Four types of movie were generated:

2.1.6.1 Rotation of aorta and human figure

Here the aorta and/or a human figure are rotated to show the position of the aorta relative to the rest of the

body. This was relatively simple and did not take very long to render (see figure 2-6).


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2.1.6.2 CT slices ‘peeling’ away to reveal model

Figure 2-6 Aorta shown with and without human reference figure

Figure 2-7 CT slices ‘peeling away’ to reveal outline and then model of the aorta


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2.1.6.3 Fly-through of the aorta

2.1.6.4 Mixture of any of the above

Combinations of the sequences above were combined together to make longer sequences; for example, a

sequence that is still under development flies around the model of the human and ‘dives’ into a flight

down the aorta.

Figure 2-8 – ‘Flight’ down the midline of the aorta


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2.2 Investigation of the effec ts of attenuating materials on or near the feed horns of

the ATCA

2.2.1 OVERVIEW

The aim of the investigation was to look into the properties of materials and the behavior of the antennas

when such materials are used to attenuate radio sources by being placed at or near the main feed horn.

Two pairs of antennas – one pair with the material and one pair without – will be used to image a strong

radio source. The outputs were compared to see for which and to what extent signals are attenuated by the

materials. It is hoped to obtain results useful for both antenna and materials engineering. The experiment

is relatively simple, the focus being on how rather than what was done. However, the results were, as

expected, widely varying and quite insightful.

2.2.2 REPORT

Please see attached report, ‘Investigation of the effects of attenuating materials on or near the feed horns

of the ATCA’. This is the report written for the project by myself on behalf of the other team members,

and is written in a ‘Journal Article’ style as we are looking at possibly getting it published.

3.0 Training

I received no formal training as such in terms of my individual project. It was my responsibility to

become familiar with the system and the development platform.

However, CSIRO, as part of the vacation scholarship program, gave us several ‘team building’ exercises.

One of the major components of such included individual grading on the TMI (Team Management Index)

system. Here we were given to opportunity to investigate how different ‘types’ of people in the workplace

interacted. For example, we discovered first hand how my ‘type’ (Creator-Innovator) clashed with the

‘Thuster-Organiser’ type and how to organise types of people to build an effective and balanced team.


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Another major team building exercise was the observatory weekend at Narrabri. Here I organised and led

a team in running a large engineering experiment on the radiotelescopes.

4.0 Relevance of Work Experience to Studies

At CSIRO, I was given invaluable exposure to the ‘real-world’ of Biomedical research. All the dry

theoretical material that I have learnt over the years at university have taken on real and significant

relevance and I have seen how my studies can be applied to a research organisation. My strong interest in

Medical Imaging and my creative preferences were given a chance to interact in a positive and useful

way.

5.0 Conclusion

I have learned how science and engineering can interact in useful ways and how remarkable research can

occur even when it is ‘profit driven’; at CSIRO, while deadlines and budgets are important, creativity is

not limited and true innovation occurs.

I was lucky enough to work with a group of enthusiastic and communicative people, who for whatever

reason share in enjoying what they are doing; the atmosphere at CSIRO is unique and hope that it stays

that way.

It has been a unique opportunity and one that I will not soon forget; I am looking forward to continuing

work there as a thesis student. My time there has been eye opening and I thoroughly recommend the

experience to any other student who is thinking of applying.

Documents

Industrial Training Report 1999-2000