Planning Thesis Production using MS Word 2007

Course Notes

IS Services, Trinity College, Dublin Presented by Niamh Hopkins ([email protected]) Contents

2 Course objectives This course is primarily designed for postgraduate students in Trinity College who are engaged in writing a research thesis. Participants completing the course will learn how to  implement the Graduate Studies Office guidelines on thesis layout using a Word template and styles – see https://www.tcd.ie/Graduate_Studies/currentstudents/admin/thesisregs/ind ex.php  set up an outline structure for the thesis with numbered headings  manage page numbering  generate table of contents, lists of tables and figures  use Section Breaks to manage page numbers, footnote numbers and page orientation

This course uses Office 2007 but the concepts outlined are all available in Office 2003. The course follows a worked example, working through the features of Word outlined above.

Templates and Master Documents – an overview

Figure 1 Figure 1 above shows the relationship between some of the main topics being covered in this course. Our first task will be to create a new template and, by modifying the styles within that template, ensure that it embodies the rules set down by the Graduate Studies Office. Any files created using this new template will have the correct margins, line spacing etc as defined by the GSO.

Creation of a Template

Our first step, then, is to create a template including settings for page margins and line spacing. Within this template we can then go on to define Styles that will control the format of the text. 1. To create a template, open a new document in Word. 2. Click on the Page Layout tab and then on the arrow to the right of the group name, Page Setup, as follows

3 Figure 2

3. Set the left margin to be not less than 35 mm and all other margins to be not less than 20 mm 4. Click Pages under multiple pages. Use the drop down arrow to choose mirror margins if your thesis is to be printed on both sides of the paper e.g. for the softbound copies. This shifts the margins so that the thesis can be bound and the margins always appear in the correct place.

4 Figure 3 5. Next save your file as a template document. 6. Click on the Office button, choose Save As and choose Word Template as follows:

5 Figure 4 7. Name your file Thesis. The file will be saved in the following folder

Figure 5

C:\Users\username\AppData\Roaming\Microsoft\Templates where ‘username’ is the username you have used to logon to your PC. To use the same template on another PC you will need to copy this file (on to a memory stick, for example) and then copy it into the equivalent location on the other PC. When moving your thesis files from one computer to another it is strongly recommended that you also move a copy of the thesis template file as well. This needs to be copied to the same folder on the destination PC.

6 Note on hidden files and folders

You may find that when browsing to the AppData folder to copy your thesis template that this folder is not visible. This Application Folder is known as a ‘hidden folder’ and on your PC is may be that hidden folders are not displayed. To change this setting follow these steps:

 when viewing any folder click on the Organize dropdown menu and choose Folder and Search Options.

 click on the View tab and tick the Show Hidden Files and Folders

Figure 6

7 Adding Style Features to a template Apart from providing a facility to control the overall appearance of your page a template can also be used to incorporate Styles which control features relating to the format of the text. These include:

 Setting the default font and font size  Setting line spacing  Setting justification

New styles can also be created to facilitate the formatting of specific pieces of text.

Setting the default font and font size

This is done by changing the font and font size of the Normal style which is the default style within a template. 1. Click on the Home tab and in the Styles group click on the arrow to the right of the group name to display the Styles window.

8 Figure 7 2. To modify the Normal style click on the dropdown arrow as above and choose Modify. 3. At this point you can choose to apply any formatting you wish using the options in the following window. For example, you could change the font size from 11 to 10. Verdana 11 point is a good choice so we will leave it as the default for the Normal style. 4. Choose to justify text in the Normal style by clicking on the Text Justify button as shown above.

Setting Line Spacing 1. Click on the Format button and choose Paragraph 2. under spacing use the drop down arrow to set the line spacing to 1.5 or double. 3. If Spacing Before or Spacing After is set to anything other than 0pt then set it to 0pt. 4. Click OK. At this point make sure that the ‘New documents based on this template’ radio button is ticked.

9 Figure 8

Heading Styles Later on we will generate a Table of Contents based on the headings in the text of the thesis. In generating this Table of Contents Word looks for text that has been set to styles Heading1, Heading 2 or Heading3. Our next step is to modify these styles so that they conform to the format we require.

1. In the Styles window click on Heading 1 and then on the dropdown arrow to the right 2. Choose Modify 3. Base Heading 1 on ‘no style’ 4. Set the font to Verdana and the point size to 14. 5. Change the text colour to Automatic (or black) 6. Choose to left justify text in the Heading 1 style. 7. In each case click the radio button ‘New documents based on this template’ but untick the ‘Automatically Update’ box.

10 Figure 9

11 Displaying all Styles At this point your Style panel may not be displaying all styles and you may not be able to see the Heading2 and Heading3 styles in the list. To display all styles- 1. Click on the Options link on the bottom right of the Styles panel 2. Choose All Styles as shown below

Figure 10

Repeat the steps outlined above for styles Heading2 and Heading 3. In doing so, base Heading 2 on Heading 1 and base Heading 3 on Heading 2. If the Heading 2 and Heading 3 styles don’t show in the list click on Options and from the dropdown list choose to show All Styles.

Editing the Caption Style In order to build lists of tables and lists of figures to accompany the table of contents for the thesis you need to use the Captions style to provide titles for tables, illustrations, graphs etc. in your thesis. The Caption style needs to be modified so that it uses the same font and font colour as the Normal style. To modify the caption style 1. Select the Caption style in the list of styles and choose Modify

12 Figure 11

2. Change the point size to 11 and bold, the colour to black and select the font to match your Normal style 3. Tick ‘New documents based on this template and click OK.

Figure 12

13 Creating a new style A style can be a useful device for quickly applying a number of formatting features to a piece of text or a table.

Creating a style for indented quotations An extended quotation in a thesis is often presented as indented from both left and right margins. To create a style called indentQuote do the following:

1. Click on the New Style button at the bottom left of the New Style window. 2. Name the style indentQuote 3. Under Format, choose Paragraph and set the left and right indent to 1.5cm and the line spacing to 1.5 as in Fig. 5. 4. To create a gap before and after an indented quote change the Before and After spacing to 6pt. 5. Don’t forget to tick ‘New documents based on this template’ 6. Click OK Figure 13 Creating a style to format tables Let’s say we have a series of tables that are typed up in the following format:

Age North South 19 69 179 20 132 438 21 57 166 29 27 44 30 185 617 31 22 19

39 7 28 40 175 617 41 13 10

Rather than displaying the data in such a plain manner we want to format it as follows:

Age North South 19 69 179 20 132 438 21 57 166 29 27 44 30 185 617 31 22 19 39 7 28 41 13 10

1. Select Styles and Formatting from the Format menu and click on New Style on the panel on the right. 2. Set up a new style called DataTable as follows: Figure 14

3. Click on the Borders button and choose Top and Bottom borders. 4. Change the Line weight to 1/4 pt. 5. Tick Add to Template and click OK.

You have now created a new style called DataTable that can be used to apply to any table you create in your documents.

Table styles are not displayed in the Styles panel alongside ‘paragraph’ styles such as Normal and Heading 1. They are only displayed when you have selected a table in the document. If you select a table and the different table styles are not displayed than click on the Table Tools tab as shown below.

Figure 15 This is consistent with the way in which commands and tools are displayed in the ribbon in Word 2007 – that is, the display of tools and commands is context sensitive. Creating a new file using the Thesis template Your new Thesis template is now ready for use. To create a new file using this template: 1. Launch MS Word and choose New from Office button 2. Click on My Templates from the panel on the left. 3. This should display something like the following

Figure 16

4. Click on ‘thesis’ and click OK. This will create a file under the thesis template. Check that the margins are correct – in particular, the left hand margin must be 3.5cms or more. Also, check that the styles you have set up in this template are available from the dropdown list on the top left corner of the Word window.

All new files that form part of your thesis should be created following these steps. Creating an outline structure using numbered headings Some disciplines require that headings in a thesis be presented as numbered. Superficially this appears to be a simple process but there are serious pitfalls and unless the numbering system is setup correctly at the start the whole system can easily go awry.

The steps we have taken already in defining our Heading styles are important, particularly the way in which Heading 2 style is based on Heading 1 and the Heading 3 style on Heading2.

To illustrate how numbered headings work we will edit our thesis template and applying outline numbers to the Heading styles.

1. Launch Word, click on the Office button and click Open 2. Click on Templates from the left hand panel and open your Thesis template 3. Click on Multilevel list in the Paragraph group of commands and then chose to link outline numbering with the Heading styles as shown

Figure 17 4. If the first line in the template file changes to a numbered Heading 1 then change it back to the Normal style. Save the change to the file and close it

You can customise how the numbers are formatted relative to the text in the headings by choosing Define New Multilevel List. The Number Position and Text Position parts of the dialog box control indents. How they work is shown below. So, set the Text Position and Number Position settings for each Level in your headings scheme.

Now, for each Level, indicate whether you want the number followed by a Tab, a Space or Nothing. When you're happy that all levels are formatted as you want, click OK, OK, Apply.

Figure 18 As we are going to use the Heading 1 style exclusively for chapter titles we can customise it to include the word Chapter so that each Heading 1 will take the format –

Chapter [number] [followed by title]

To do this edit Heading 1 as follows- Having applied these number formats to Headings you can now get the following overview of your file by choosing Outline from the View menu and from the Show Level dropdown menu choose Show Level 3.

Merging Files A Ph.D. thesis can extend to 100,000 words and it makes sense to divide up such a long piece of work, consisting of many chapters, into a number of separate files. The problem with having your work spread over a number of files is that it means you can’t use the Table of Contents and Table of Figures features of Word to automatically generate these tables, as we will do later in the course. Structuring your work in this way also makes the management of page numbers an additional task. An approach that could be used is to type up the different sections of your thesis in separate files – remembering to create each file under your ‘thesis’ template. When you are close to completing your thesis you can then merge these files together using a series of Select All – Copy – Paste operations.

This approach make cause problem is the merged Word file is very large – say 8 or 10 Mb. A document consisting exclusively of text is very unlikely to reach this size. However, if your thesis contains scanned images, particularly if they are of a high resolution, this is likely to add considerable to the overall file size. In these circumstances the Master Document / Sub-Document approach described in the full IS Services course is recommended.

For example, let’s say the thesis consists of the following files Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 To merge these files into one new file do the following: 1. Create a new file using your thesis template and save it as Complete Thesis 2. Open Chapter 1 3. Select all the contents as shown Figure 19

4. Click Copy 5. Switch back to the Complete Thesis file 6. Click Paste 7. Open Chapter 2 8. Select all the contents as shown 9. Click Copy 10. Switch back to the Complete Thesis file. Make sure the insertion point is at the end of the file. 11. Click Paste 12. Open Chapter 3 13. Select all the contents as shown 14. Click Copy 15. Switch back to the Complete Thesis file. Make sure the insertion point is at the end of the file. 16. Click Paste 17. Open Chapter 4 18. Select all the contents as shown 19. Click Copy 20. Switch back to the Complete Thesis file. Make sure the insertion point is at the end of the file. 21. Click Paste 22. Open Chapter 5 23. Select all the contents as shown 24. Click Copy 25. Switch back to the Complete Thesis file. Make sure the insertion point is at the end of the file. 26. Click Paste

Adding Page Numbers to Merged File Managing page numbers is done using the Headers and Footers. Page numbers should be centred in the footer.

Click on Insert and then on Page Number in the Header & Footer group Choose the option shown below

Figure 20

Apply Styles and Insert Captions Scroll through the merged file and apply the Heading 1 style to the chapter headings, apply the Heading 2 style to the main sub-headings and apply the Heading 3 style to some of the sub-headings in Chapters 4 and 5.

To insert captions click on the References tab and below each table and figure 1. Click Insert caption 2. If the object is a table choose label type ‘table’. If the object is a figure choose label type ‘figure. 3. Remove the tick beside ‘Exclude label from caption’ 4. Click Numering and choose to include the chapter number. This option is only applicable if you are using numbered headings. When you’ve finished these steps insert three blank pages at the beginning of the file to prepare for the insert of the table of contents and other lists. Table of Contents A Table of Contents should immediately follow your acknowledgements page. It's basically a list of what's in your thesis but according to the Graduate Studies Office guidelines it should-

'Show list in sequence, with page numbers, all relevant subdivisions of the thesis, including the list of abbreviations, titles of chapters and their sections and subsections ;the list of references; the bibliography (if any), other functional parts of the whole thesis; and any appendices and the index (if provided)'

A Table of Contents will pick up on the Headings defined in a document and uses these to build the table

To insert a Table of Contents 1. First, insert a page break at the beginning of the file by choosing Insert -> Page Break. 2. Choose References and then Table of Contents. Click on the down-arrow and choose Insert Table of Contents so you get to manually set the format of the table 3. From the Table of Contents dialogue box shown below choose whether to Show page numbers, whether to Right align page numbers, choose a Tab leader, and a Format and decide using Show levels the number of levels to be seen. View results in Print Preview. Click OK to accept results. Figure 21

Changes to the text of the thesis – whether the text in headings of addition/removal of text affecting page numbering – will be not automatically reflected in the table of contents. Having made a change of this type you need to manually update the table of contents. To do this simply highlight it clicking in the table of contents and then press the function key F9 (or right mouse click and choose Update Field or Update Entire Table). Click OK.

With the Control key depressed you can navigate the Table of Contents by clicking on any item in it. To return to the top of the file press Ctrl and the Home key.

Tables of Tables and Figures Following the table of contents it is customary to include a list of tables and a separate list of figures included in the thesis. As with a Table of Contents, these can be automatically generated using the relevant features in Word.

1. At the top of page 2 type in the heading ‘List of tables’ 2. Apply the Initial style to this text 3. Choose References -> Insert Table of Figures 4. For your list of tables choose Tables from the dropdown list beside ‘Caption label’ 5. Insert a page break and type in the heading ‘List of figures’ on the new page. 6. Choose References -> Insert Table of Figures 7. For your list of figures choose Figures from the dropdown list beside ‘Caption label’

Appendix 1

‘NEW’ THESIS SUBMISSION GUIDELINES FOR STUDENTS REGISTERED FROM SEPTEMBER 2009

1.32.1 General. Candidates and Supervisors should note that these requirements are mandatory and they are asked to familiarise themselves with the information below. Theses’ must meet all the requirements set out below. Please note: from time to time the Dean of Graduate Studies may approve other formats on an individual basis.

1.32.2 Language. A thesis or dissertation should be written in English or Irish unless prior permission has been granted for the use of another language by the Dean of Graduate Studies. A candidate who wishes to write a thesis or dissertation in a language other than English or Irish should initially contact his/her Supervisor/Course Co-ordinator. The Supervisor/Course Coordinator will then consult with his/her Director of Teaching and Learning (Postgraduate). If the latter can satisfy him/herself that a) there are sound academic reasons for the thesis or dissertation to be written in a language other than English or Irish and b) that the candidate has the necessary skills/fluency in the relevant language, then the Director of Teaching and Learning (Postgraduate) should send a summary of the case under the two headings outlined above to the Dean of Graduate Studies. The Dean of Graduate Studies will normally be guided by the recommendation of the Director of Teaching and Learning (Postgraduate), but may refer the matter to the Graduate Studies Committee if s/he deems it necessary.

1.32.3 Published Work. A thesis submitted for a higher degree may be based on, or include, writings already published by the candidate, if the studies from which they derive have been carried out during the period of registration on the higher degree register. Such writings must be fully integrated into the body of the thesis.

1.32.4 Length. A thesis must be written concisely. There is no minimum length for a Ph.D. or Masters (M.Litt. or M.Sc. by research) thesis. Dissertations submitted in part-fulfilment of the requirements of a postgraduate taught course are limited to the length prescribed in the individual course regulations. Normally a Ph.D. thesis should not exceed 100,000 words of text and an M.Litt. or an M.Sc. (by research) thesis, 60,000 words of text, and for scientific or technical subjects will normally be shorter. If a thesis is likely to exceed these limits, the Dean of Graduate Studies must be advised of its estimated length and her/his permission obtained at an early stage in the writing. Additional material, such as numerical appendices, listings of computer programs and textual footnotes, may be bound in a separate volume. Where the combined length of text, footnotes and appendices, etc. exceeds 400 pages the thesis must be bound in two volumes.

1.32.5 Typescript and illustrations. The thesis must be printed on good quality, A4 (297 x 210mm) white paper. The type must be fully formed as in the output of a laser or ink jet printer. The output of dot matrix printers is not acceptable. The type must be black and not less than 10 point. Line-spacing must be at one and a half or double spacing between lines. The gutter margin of both text and diagrams must not be less than 35 mm and that on the other three sides not less than 20 mm. The two copies of the thesis for examination should be soft-bound and printed on one side of the page only. It is expected that the hard-bound copy of a thesis will be printed on both sides of the page on paper of a weight of at least 90 gsm. A copy of the hard-bound thesis will be lodged in the Library following approval by Council. Colour photocopies and scanned images may be used in the copy of the thesis deposited in the Library.

1.32.6 Cover. A thesis which has been examined and in which all necessary corrections have been completed must be securely bound in hard covers with dark blue cloth. The final size when bound must not exceed 320 x 240 mm.

1.32.7 Title. The title of the thesis must be written in full on the title page of each volume of the thesis. The degree for which the thesis has been submitted, the year, and the name of the candidate, in that order, should be lettered in gold, in 24 pt or larger type, down the spine, so as to be readable when the volume is lying flat with the front cover uppermost. The title must also appear in gold lettering on the front cover of the thesis. The year on the spine and title page must be the year that the thesis was approved by Council (not the year of initial submission).

1.32.8 Declaration. The thesis must contain immediately after the title page a signed declaration that a) it has not been submitted as an exercise for a degree at this or any other University, b) it is entirely the candidate's own work (in the case of a thesis for which the work has been carried out jointly; there must be a statement that it includes the unpublished and/or published work of others, duly acknowledged in the text wherever included) and c) the candidate agrees that the Library may lend or copy the thesis upon request. This permission covers only single copies made for study purposes, subject to normal conditions of acknowledgement. (See below for withheld access (a “stay”) for such permission).

1.32.9 Summary. A succinct summary of the methods used and the major findings of the thesis must be bound into each copy of the thesis following the declaration page. It must not exceed two pages of typescript.

1.32.10 Acknowledgements. A formal statement of acknowledgements must be included in the thesis.

1.32.11 References. Systematic and complete reference to sources used and a classified list of all sources used must be included in the thesis. The titles of journals preferably should not be abbreviated; if they are, abbreviations must comply with an internationally recognised system (the format may vary according to the precedents and customs of the subject area; graduate students should consult with their Supervisor as to appropriate presentation).

1.32.12 Abstract. One copy of an abstract, printed on a single sheet of A4 paper, must be submitted loose with each copy of the soft-bound thesis. The abstract must contain the title of the thesis and the author's full names as a heading and may be single spaced. Two copies of an abstract must be submitted loose with the final hard-bound copy.

1.32.13 Submission. Two copies of the thesis, which may not be returned, and which for the first submission must be soft-bound, should be presented at the Graduate Studies Office, accompanied by two loose copies of the abstract. The thesis will not be accepted until it has been established that the candidate is currently registered on the higher degree register and that any outstanding fees have been paid.

1.32.14 Access to theses’. One copy of every thesis approved for a higher degree is lodged in the custody of the Librarian in the University Library. A thesis so approved may be consulted or copied in the Library or through an inter-library loan. Users must undertake not to use or reproduce material so obtained without the consent of the Librarian and must acknowledge duly the source of such information.

1.32.15 Withheld access (a “stay”). Should an author of a thesis wish to withhold permission for the use of her/his work, a written application must be made to the Dean of Graduate Studies at the time of submission of the thesis for examination. Such applications must have the written support of the graduate student's Supervisor or Director of Teaching and Learning (Postgraduate), must state the reasons for the request for a stay on access and must provide a contact address. The maximum length of a stay is five years. During this period of withheld permission the thesis may be consulted, lent or copied only by written permission of the author who is under an obligation to reply to all inquiries within a reasonable time.

Dean’s Grace and Submission Deadlines Please note that the normal deadline for thesis submission is 30 August for September registrants and 1 March for March registrants. However, if you require Dean’s Grace of one month extension (free of fees) to submit your thesis normally by 30 September or 31 March respectively you must put your request via your supervisor before 30 August or 1 March respectively who should email the Dean of Graduate Studies directly at [email protected] Appendix 2

A Statistical Approach to Signal Processing Techniques In Post-Production Systems

A dissertation submitted to the University of Dublin for the Degree of Doctor of Philosophy James Burnside

Trinity College Dublin, November 2006 Department of Electrical Engineering Trinity College Dublin Declaration

I hereby declare that this thesis has not been submitted as an exercise for a degree at this or any other University and that it is entirely my own work. I agree that the Library may lend or copy this thesis upon request.

Signed, James Redmond November 21, 2008 Summary Nonlinear Signal Processing: A Statistical Approach focuses on unifying the study of a broad and important class of nonlinear signal processing algorithms which emerge from statistical estimation principles, and where the underlying signals are non- Gaussian, rather than Gaussian, processes. Notably, by concentrating on just two non-Gaussian models, a large set of tools is developed that encompass a large portion of the nonlinear signal processing tools proposed in the literature over the past several decades.

Key features include:

* Numerous problems at the end of each chapter to aid development and understanding * Examples and case studies provided throughout the book in a wide range of applications bring the text to life and place the theory into context * A set of 60+ MATLAB software m-files allowing the reader to quickly design and apply any of the nonlinear signal processing algorithms described in the book to an application of interest is available on the accompanying FTP site. Acknowledgments I would like to thank all former and present members of the Visualization group who have helped me over the years, and especially my PhD companions: and Dr. Francis Kelly.

I wish to express my deep gratitude to my co-supervisor Dr. Kiera Russell for the time she gave me. And of course, most of all, I would like to thank my supervisor Dr. William Bentley for his patience and intelligence in deciphering my obscure drafts, the good atmosphere he instigates in the lab, his contagious motivation and, above all, his constant efforts and help over the last 3 years. Thanks Anil.

And of course, I wish to thank my parents, my brothers and all my friends for their love and support and the good time I had in Dublin. Contents Introduction 1 Transfer of Statistics in Image Processing 9 Probabilistic Tracking 19 Image Simpli fication 25 Thesis Outline 30 Distribution Transfer and its Applications 38 Distribution Transfer 41 The Linear Case 49 The General Non-Linear Case 60 The 1D case 69 Extending the 1D Case to Higher Dimensions 78 Description of the Manipulation . 90 Theoretical Convergence Study 104 Kullback-Leibler Divergence 111 Experimental Datasets: Sampling PDFs 123 Results and Choice of Axis Sequence 130 Conclusion 140 Appendix 129 Tables 1.1 Introduction 1 2.1 Transfer of Statistics in Image Processing 9 2.2 Probabilistic Tracking 19 2.3 Image Simpli fication 25 2.4 Thesis Outline 30 2.5 Distribution Transfer and its Applications 38 3.1 Distribution Transfer 41 3.2 The Linear Case 49 3.3 The General Non-Linear Case 60 3.4 The 1D case 69 4.1 Extending the 1D Case to Higher Dimensions 78 5.1 Description of the Manipulation . 90 5.2 Theoretical Convergence Study 104 5.3 Kullback-Leibler Divergence 111 6.1 Experimental Datasets: Sampling PDFs 123 7.1 Results and Choice of Axis Sequence 130 Figures 3.1 Distribution Transfer and its Applications 38 3.2 Distribution Transfer 41 3.3 The Linear Case 49 4.1 The General Non-Linear Case 60 4.2 The 1D case 69 5.1 Extending the 1D Case to Higher Dimensions 78 5.2 Description of the Manipulation . 90 6.2 Theoretical Convergence Study 104 6.3Kullback-Leibler Divergence 111 7.1 Experimental Datasets: Sampling PDFs 123