changeset 2054:a164db84aaef

Merge

--- a/.hgignore	Sun Jun 28 09:52:47 2015 +0100
+++ b/.hgignore	Mon Jun 29 19:04:40 2015 +0100
@@ -24,3 +24,6 @@
 re:^example_eval/project\.xml\.orig$
 re:^index2\.html$
 re:^realismTest\.html$
+saves/*.xml
+saves/timelines
+saves/timelines-old
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CITING.txt	Mon Jun 29 19:04:40 2015 +0100
@@ -0,0 +1,11 @@
+If you are using this tool in your work, please cite: 
+
+Nicholas Jillings, Brecht De Man, David Moffat and Joshua D. Reiss, "Web Audio Evaluation Tool: A Browser-Based Listening Test Environment," 12th Sound and Music Computing Conference, July 2015.
+
+
+Feel free to let us know how you have used it! We highly welcome any kind of feedback, bug reports and feature requests. 
+
[e-mail]
[e-mail]
[e-mail]
[e-mail]
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE.txt	Mon Jun 29 19:04:40 2015 +0100
@@ -0,0 +1,674 @@
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+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Mon Jun 29 19:04:40 2015 +0100
@@ -0,0 +1,92 @@
+WEB AUDIO EVALUATION TOOL
+
+This is not (yet) a fully fledged manual. 
+
+
+AUTHORS
+Nicholas Jillings 		<[e-mail]>
+Brecht De Man			<[e-mail]>
+David Moffat			<[e-mail]>
+Joshua D. Reiss (supervisor)	<[e-mail]>
+
+
+PACKAGE CONTENTS
+
+- main folder (/)
+	- ape.css, core.css, graphics.css, structure.css: style files (edit to change appearance)
+	- ape.js: JavaScript file for APE-style interface [1]
+	- core.js: JavaScript file with core functionality
+	- index.html: webpage where interface should appear
+	- jquery-2.1.4.js: jQuery JavaScript Library
+	- pythonServer.py: webserver for running tests locally
+	- pythonServer-legacy.py: webserver with limited functionality (no storing of output XML files)
+- Documentation (/docs/)
+	- Project Specification Document (LaTeX/PDF)
+	- Results Specification Document (LaTeX/PDF)
+	- SMC15: PDF and LaTeX source of corresponding SMC2015 publication
+- Example project (/example_eval/)
+	An example of what the set up XML should look like, with example audio files 0.wav-10.wav which are short recordings at 44.1kHz, 16bit of a woman saying the corresponding number (useful for testing randomisation and general familiarisation with the interface). 
+- Output files (/saves/)
+	The output XML files of tests will be stored here by default by the pythonServer.py script. 
+- Auxiliary scripts (/scripts/)
+	Helpful Python scripts for extraction and visualisation of data. 
+- Test creation tool (/test_create/)
+	Webpage for easily setting up a test without having to delve into the XML. 
+
+
+QUICK START
+Using the example project: 
+1. Make sure your system sample rate corresponds with the sample rate of the audio files, if the input XML file enforces the given sample rate. 
+2. Run pythonServer.py (make sure you have Python installed). 
+3. Open a browser (anything but Internet Explorer). 
+4. Go to ‘localhost:8000’. 
+5. The test should open; complete it and look at the output XML file in /saves/. 
+
+
+LEGACY
+The APE interface and most of the functionality of the interface is inspired by the APE toolbox for MATLAB [1]. See https://code.soundsoftware.ac.uk/projects/ape for the source code and corresponding paper. 
+
+
+CITING
+
+We request that you acknowledge the authors and cite our work [2], see CITING.txt. 
+
+
+LICENSE
+
+See LICENSE.txt. This code is shared under the GNU General Public License v3.0 (http://choosealicense.com/licenses/gpl-3.0/). Generally speaking, this is a copyleft license that requires anyone who distributes our code or a derivative work to make the source available under the same terms. 
+
+
+FEATURE REQUESTS AND BUG REPORTS
+We continually develop this tool to fix issues and implement features useful to us or our user base. See https://code.soundsoftware.ac.uk/projects/webaudioevaluationtool/issues for a list of feature requests and bug reports, and their status. 
+
+Please contact the authors if you experience any bugs, if you would like additional functionality, if you have questions about using the interface or if you would like to give any feedback (even positive!) about the interface. We look forward to learning how the tool has (not) been useful to you. 
+
+
+SCRIPTS
+
+The tool comes with a few handy Python scripts for easy extraction of ratings or comments, and visualisation of ratings and timelines. See below for a quick guide on how to use them. All scripts written for Python 2.7. Visualisation requires the free matplotlib toolbox (http://matplotlib.org), numpy and scipy. 
+By default, the scripts can be run from the ‘scripts’ folder, with the result files in the ‘saves’ folder (the default location where result XMLs are stored). 
+
+	comment_parser.py
+		Extracts comments from the output XML files corresponding with the different subjects found in ‘saves/’. It creates a folder per ‘audioholder’/page it finds, and stores a CSV file with comments for every ‘audioelement’/fragment within these respective ‘audioholders’/pages. In this CSV file, every line corresponds with a subject/output XML file. Depending on the settings, the first column containing the name of the corresponding XML file can be omitted (for anonymisation). 
+		Beware of Excel: sometimes the UTF-8 is not properly imported, leading to problems with special characters in the comments (particularly cumbersome for foreign languages). 
+
+	score_parser.py
+		Extracts rating values from the XML to CSV - necessary for running visualisation of ratings. Creates the folder ‘saves/ratings/‘ if not yet created, to which it writes a separate file for every ‘audioholder’/page in any of the output XMLs it finds in ‘saves/‘. Within each file, rows represent different subjects (output XML file names) and columns represent different ‘audioelements’/fragments. 
+
+	score_plot.py
+		Plots the ratings as stored in the CSVs created by score_parser.py
+		Depending on the settings, it displays and/or saves (in ‘saves/ratings/’) a boxplot, confidence interval plot, scatter plot, or a combination of the aforementioned. 
+		Requires the free matplotlib library. 
+		At this point, more than one subjects are needed for this script to work. 
+
+	timeline_view.py
+		Creates a timeline for every subject, for every ‘audioholder’/page, corresponding with any of the output XML files found in ‘/saves’. It shows when and for how long the subject listened to each of the fragments. 
+
+
+
+REFERENCES
+[1] B. De Man and Joshua D. Reiss, “APE: Audio Perceptual Evaluation toolbox for MATLAB,” 136th Convention of the Audio Engineering Society, 2014.
+
+[2] Nicholas Jillings, Brecht De Man, David Moffat and Joshua D. Reiss, "Web Audio Evaluation Tool: A Browser-Based Listening Test Environment," 12th Sound and Music Computing Conference, July 2015.

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--- a/docs/SMC15/smc2015template.tex	Sun Jun 28 09:52:47 2015 +0100
+++ b/docs/SMC15/smc2015template.tex	Mon Jun 29 19:04:40 2015 +0100
@@ -10,9 +10,19 @@
 \usepackage[english]{babel}
 \usepackage{cite}
 \usepackage{enumitem}
+\usepackage{listings}
 \setitemize{noitemsep,topsep=0pt,parsep=0pt,partopsep=0pt}
 
+
+
+\usepackage{color}
+\definecolor{grey}{rgb}{0.1,0.1,0.1}
+\definecolor{darkblue}{rgb}{0.0,0.0,0.6}
+\definecolor{cyan}{rgb}{0.0,0.6,0.6}
+
+
 \hyphenation{Java-script}
+\hyphenation{OPA-QUE}
 
 %%%%%%%%%%%%%%%%%%%%%%%% Some useful packages %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%% See related documentation %%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -189,7 +199,7 @@
 Many are MATLAB-based, useful for easily processing and visualising the data produced by the listening tests, but requiring MATLAB to be installed to run or - in the case of an executable created with MATLAB - at least create the test. 
 Furthermore, compatibility is usually limited across different versions of MATLAB. 
 Similarly, Max requires little or no programming background but it is proprietary software as well, which is especially undesirable when tests need to be deployed at different sites.
-More recently, BeaqleJS \cite{beaqlejs} makes use of the HTML5 audio capabilities and comes with a number of predefined, established test interfaces such as ABX and MUSHRA \cite{mushra}. BeaqleJS provides a number of similar features including saving of test data to a web server. The main difference is that with BeaqleJS, the configuration is done through writting a JavaScript file holding a JavaScript Object of the notation. Instead our presented system uses the XML document standard, which allows configuration outside of a web-centric editor. The results are also presented in XML again allowing 3rd party editors and programs to easily access. Finally, the presented system does not require web access to run, instead being deployed with a Python server script. This is particularly useful in studios where machines may not, by design, be web connected, or use in locations where web access is limited.
+More recently, BeaqleJS \cite{beaqlejs} makes use of the HTML5 audio capabilities and comes with a number of predefined, established test interfaces such as ABX and MUSHRA \cite{mushra}. BeaqleJS provides a number of similar features including saving of test data to a web server. The main difference is that with BeaqleJS, the configuration is done through writting a JavaScript file holding a JavaScript Object of the notation. Instead our presented system uses the XML document standard, which allows configuration outside of a web-centric editor. The results are also presented in XML again allowing 3\textsuperscript{rd} party editors and programs to easily access. Finally, the presented system does not require web access to run, instead being deployed with a Python server script. This is particularly useful in studios where machines may not, by design, be web connected, or use in locations where web access is limited.
 
 A browser-based perceptual evaluation tool for audio has a number of advantages. First of all, it doesn't need any other software than a browser, meaning deployment is very easy and cheap. As such, it can also run on a variety of devices and platforms. The test can be hosted on a central server with subjects all over the world, who can simply go to a webpage. This means that multiple participants can take the test simultaneously, potentially in their usual listening environment if this is beneficial for the test. Naturally, the constraints on the listening environment and other variables still need to be controlled if they are important to the experiment. Depending on the requirements a survey or a variety of tests preceding the experiment could establish whether remote participants and their environments are adequate for the experiment at hand. 
 
@@ -220,8 +230,6 @@
 %\begin{itemize}
 %\item 
 %\end{itemize}
-
-
 \section{Interface}\label{sec:interface}
 
 At this point, we have implemented the interface of the MATLAB-based APE (Audio Perceptual Evaluation) toolbox \cite{deman2014b}. This shows one marker for each simultaneously evaluated audio fragment on one or more horizontal axes, that can be moved to rate or rank the respective fragments in terms of any subjective property, as well as a comment box for every marker, and any extra text boxes for extra comments. 
@@ -229,7 +237,7 @@
 
 The markers on the slider at the top of the page are positioned randomly, to minimise the bias that may be introduced when the initial positions are near the beginning, end or middle of the slider. Another approach is to place the markers outside of the slider bar at first and have the subject drag them in, but the authors believe this doesn't encourage careful consideration and comparison of the different fragments as the implicit goal of the test becomes to audition and drag each fragment in just once, rather than to compare all fragments rigorously.
 
-See Figure \ref{fig:interface} for an example of the interface, with six fragments and one axis. %? change if a new interface is shown
+See Figure \ref{fig:interface} for an example of the interface. %? change if a new interface is shown
 
 %Most of these functions are specific to the APE interface design, for instance the AB test will need a different structure for the audio engine and loading of files, since multiple instances of the same file are required. % more generally these pertain to any typeof multi-stimulus test - not quite useful for AB tests, method of adjustment, ABX, and so on. 
 %There are some areas of the design where certain design choices had to be made such as with the markers. 
@@ -237,11 +245,10 @@
 %For instance, the option to provide free-text comment fields allows for tests with individual vocabulary methods, as opposed to only allowing quantitative scales associated to a fixed set of descriptors.
 
 \begin{figure*}[ht]
-\begin{center}
-\includegraphics[width=1.0\textwidth]{interface2.png}
-\caption{Example of interface, with 1 axis, 6 fragments and 1 extra comment in Chrome browser}
+\centering
+\includegraphics[width=.95\textwidth]{interface.png}
+\caption{Example interface, with one axis, seven fragments, and text, radio button and check box style comments.}
 \label{fig:interface}
-\end{center}
 \end{figure*}
 
 
@@ -256,22 +263,24 @@
 \item \texttt{ape.js}: Parses setup files to create the interface as instructed, following the same style chain as the MATLAB APE Tool \cite{deman2014b}.
 \end{itemize}
 
-The HTML file loads the \texttt{core.js} file along with a few other ancillary files (such as the jQuery JavaScript extensions\footnote{http://jquery.com/}), at which point the browser JavaScript begins to execute the on-page instructions, which gives the URL of the test setup XML document (outlined in Section \ref{sec:setupresultsformats}). \texttt{core.js} parses this document and executes the functions in \texttt{ape.js} to build the web page. The reason for separating these two files is to allow for further interface designs (such as MUSHRA \cite{mushra} or AB tests \cite{bech}) to be used, which would still require the same underlying core functions outlined in \texttt{core.js}.
+The HTML file loads the \texttt{core.js} file along with a few other ancillary files (such as the jQuery JavaScript extensions\footnote{http://jquery.com/}), at which point the browser JavaScript begins to execute the on-page instructions, which gives the URL of the test setup XML document (outlined in Section \ref{sec:setupresultsformats}). \texttt{core.js} parses this document and executes the functions in \texttt{ape.js} to build the web page. The reason for separating these two files is to allow for further interface designs (such as MUSHRA \cite{mushra} or 2D rating \cite{bech}) to be used, which would still require the same underlying core functions outlined in \texttt{core.js}.
 
 The \texttt{ape.js} file has several main functions but the most important are documented here. \textit{loadInterface(xmlDoc)} is called to decode the supplied project document in respect for the interface specified and define any global structures (such as the slider interface). It also identifies the number of pages in the test and randomises the order, if specified to do so. This is the only mandatory function in any of the interface files as this is called by \texttt{core.js} when the document is ready. \texttt{core.js} cannot 'see' any interface specific functions and therefore cannot assume any are available. Therefore \textit{loadInterface(xmlDoc)} is essential to set up the entire test environment. Because the interface files are loaded by \texttt{core.js} and because the functions in \texttt{core.js} are global, the interface files can `see' the \texttt{core.js} file and can therefore not only interact with it, but also modify it.
 
 Each test page is loaded using \textit{loadTest(id)} which performs two major tasks: to populate the interface with the slider elements and comment boxes; and secondly to instruct the \textit{audioEngine} to load the audio fragments and construct the backend audio graph. \textit{loadTest(id)} also instructs the audio engine in \texttt{core.js} to create the \textit{audioObject}. 
 These are custom audio nodes, one representing each audio element specified in each page.
-They consist of a \textit{bufferSourceNode} (a node which holds a buffer of audio samples for playback) and a \textit{gainNode}, both of which are Web Audio API Nodes. Various functions are applied, depending on which metrics are enabled, to record the interaction with the audio element. These nodes are then connected to the \textit{audioEngine} (itself a custom web audio node) containing a \textit{gainNode} (where the various \textit{audioObject}s connect to) for summation before passing the output to the \textit{destinationNode}, a permanent node of the Web Audio API created as the master output. Here, the browser then passes the audio information to the system sound device. % Does this now make sense?
+They consist of a \textit{bufferSourceNode} (a node which holds a buffer of audio samples for playback) and a \textit{gainNode}, both of which are Web Audio API Nodes. Various functions are applied, depending on which metrics are enabled, to record the interaction with the audio element. These nodes are then connected to the \textit{audioEngine} (itself a custom web audio node) containing a \textit{gainNode} (where the various \textit{audioObject}s connect to) for summation before passing the output to the \textit{destinationNode}, a permanent node of the Web Audio API created as the master output. Here, the browser then passes the audio information to the system. % Does this now make sense?
 % audio object/audioObject/Audio Object: -- should always be audioObject if talking about the JavaScript object, otherwise should say audio element or audio fragment.
 
 When an \textit{audioObject} is created, it is given the URL of the audio sample to load. This is downloaded into the browser asynchronously using the \textit{XMLHttpRequest} object, which downloads any file into the JavaScript environment for further processing. This is particularly useful for the Web Audio API because it supports downloading of files in their binary form for decoding. Once downloaded the file is decoded using the Web Audio API offline decoder. This uses the browser available decoding schemes to decode the audio files into raw float32 arrays, which are in turn passed to the relevant \textit{audioObject} for playback.
 
 Once each page of the test is completed, identified by pressing the Submit button, the \textit{pageXMLSave(testId)} is called to store all of the collected data until all pages of the test are completed. After the final test and any post-test questions are completed, the \textit{interfaceXMLSave()} function is called. This function generates the final XML file for submission as outlined in Section \ref{sec:setupresultsformats}.
 
+\vspace{-1em}
+
 \section{Support and limitations}\label{sec:support}
 
-Browsers support various audio file formats and are not consistent in any format. Currently the Web Audio API is best supported in Chrome, Firefox, Opera and Safari. All of these support the use of the uncompressed WAV format. Although not a compact, web friendly format, most transport systems are of a high enough bandwidth this should not be a problem. Ogg Vorbis is another well supported format across the four supported major desktop browsers, as well as MP3 (although Firefox may not support all MP3 types) \footnote{https://developer.mozilla.org/en-US/docs/Web/HTML/\\Supported\_media\_formats}. %https://developer.mozilla.org/en-US/docs/Web/HTML/Supported_media_formats
+Different browsers support a different set of audio file formats and are not consistent in any format. Currently the Web Audio API is best supported in Chrome, Firefox, Opera and Safari. All of these support the use of the uncompressed WAV format. Although not a compact, web friendly format, most transport systems are of a high enough bandwidth this should not be a problem. Ogg Vorbis is another well supported format across the four supported major desktop browsers, as well as MP3 (although Firefox may not support all MP3 types\footnote{https://developer.mozilla.org/en-US/docs/Web/HTML/\\Supported\_media\_formats}). %https://developer.mozilla.org/en-US/docs/Web/HTML/Supported_media_formats
 One issue of the Web Audio API is that the sample rate is assigned by the system sound device, rather than requested and does not have the ability to request a different one. % Does this make sense? The problem is across all audio files.
 As the sampling rate and the effect of resampling may be critical for some listening tests, the default operation when an audio file is loaded with a different sample rate to that of the system is to convert the sample rate. To provide a check for this, the desired sample rate can be supplied with the setup XML and checked against. If the sample rates do not match, a browser alert window is shown asking for the sample rate to be correctly adjusted. 
 This happens before any loading or decoding of audio files so the browser will only be instructed to fetch files if the system sample rate meets the requirements, avoiding multiple requests for large files until they are actually needed.
@@ -282,41 +291,103 @@
 
 \section{Input and result files}\label{sec:setupresultsformats}
 
-The setup and result files both use the common XML document format to outline the various parameters. The setup file determines the interface to use, the location of audio files, the number of pages and other parameters to define the testing environment. Having one document to modify allows for quick manipulation in a `human readable' form to create new tests, or adjust current ones, without needing to edit multiple web files. Furthermore, we also provide a simple web page to enter all these settings without needing to manipulate the raw XML. An example of this XML document is presented in Figure~\ref{fig:xmlIn}. % I mean the .js and .html files, though not sure if any better.
+The setup and result files both use the common XML document format to outline the various parameters. The setup file determines the interface to use, the location of audio files, the number of pages and other parameters to define the testing environment. Having one document to modify allows for quick manipulation in a `human readable' form to create new tests, or adjust current ones, without needing to edit multiple web files. Furthermore, we also provide a simple web page to enter all these settings without needing to manipulate the raw XML. An example of such an XML document is presented below. % I mean the .js and .html files, though not sure if any better.
+
+
+
+
+\lstset{
+  basicstyle=\ttfamily,
+  columns=fullflexible,
+  showstringspaces=false,
+  commentstyle=\color{grey}\upshape
+}
+
+\lstdefinelanguage{XML}
+{
+  morestring=[b]",
+  morestring=[s]{>}{<},
+  morecomment=[s]{<?}{?>},
+  stringstyle=\color{black} \bfseries,
+  identifierstyle=\color{darkblue} \bfseries,
+  keywordstyle=\color{cyan} \bfseries,
+  morekeywords={xmlns,version,type}, 
+  breaklines=true% list your attributes here
+}
+\scriptsize
+\lstset{language=XML}
+
+\begin{lstlisting}
+<?xml version="1.0" encoding="utf-8"?>
+<BrowserEvalProjectDocument>
+	<setup interface="APE" projectReturn="/save" randomiseOrder='false' collectMetrics='true'>
+		<PreTest>
+			<question id="location" mandatory="true">Please enter your location.</question>
+			<number id="age" min="0">Please enter your age</number>
+		</PreTest>
+		<PostTest>
+			<statement>Thank you for taking this listening test!</statement>
+		</PostTest>
+		<Metric>
+			<metricEnable>testTimer</metricEnable>
+			<metricEnable>elementTimer</metricEnable>
+			<metricEnable>elementInitialPosition</metricEnable>
+			<metricEnable>elementTracker</metricEnable>
+			<metricEnable>elementFlagListenedTo</metricEnable>
+			<metricEnable>elementFlagMoved</metricEnable>
+		</Metric>
+		<interface>
+			<anchor>20</anchor>
+			<reference>80</reference>
+		</interface>
+	</setup>
+	<audioHolder id="test-0" hostURL="example_eval/" randomiseOrder='true'>
+		<interface>
+			<title>Example Test Question</title>
+			<scale position="0">Min</scale>
+			<scale position="100">Max</scale>
+			<commentBoxPrefix>Comment on fragment</commentBoxPrefix>
+		</interface>
+		<audioElements url="1.wav" id="elem1"/>
+		<audioElements url="2.wav" id="elem2"/>
+		<audioElements url="3.wav" id="elem3"/>
+		<CommentQuestion id="generalExperience" type="text">General Comments</CommentQuestion>
+		<PreTest/>
+		<PostTest>
+			<question id="songGenre" mandatory="true">Please enter the genre of the song.</question>
+		</PostTest>
+	</audioHolder>
+</BrowserEvalProjectDocument>
+
+\end{lstlisting}
+
+\normalsize
+\vspace{-1em}
 
 \subsection{Setup and configurability}
 
-\begin{figure}[ht]
-\begin{center}
-\includegraphics[width=0.5\textwidth]{XMLInput2.png}
-\caption{An example input XML file}
-\label{fig:xmlIn}
-\end{center}
-\end{figure}
-
-The setup document has several defined nodes and structure which are documented with the source code. For example, there is a section for general setup options where any pre-test and post-test questions and statements can be defined. Pre- and post-test dialogue boxes allow for comments or questions to be presented before or after the test, to convey listening test instructions, and gather information about the subject, listening environment, and overall experience of the test. In the example in Figure~\ref{fig:xmlIn}, a question box with the id `location' is added, which is set to be mandatory to answer. The question is in the PreTest node meaning it will appear before any testing will begin. When the result for the  entire test is shown, the response will appear in the PreTest node with the id `location' allowing it to be found easily, provided the id values are meaningful.
+The setup document has several defined nodes and structure which are documented with the source code. For example, there is a section for general setup options where any pre-test and post-test questions and statements can be defined. Pre- and post-test dialogue boxes allow for comments or questions to be presented before or after the test, to convey listening test instructions, and gather information about the subject, listening environment, and overall experience of the test. In the example set up document above, a question box with the id `location' is added, which is set to be mandatory to answer. The question is in the PreTest node meaning it will appear before any testing will begin. When the result for the  entire test is shown, the response will appear in the PreTest node with the id `location' allowing it to be found easily, provided the id values are meaningful.
 
 We try to cater to a diverse audience with this toolbox, while ensuring it is simple, elegant and straightforward. To that end, we currently include the following options that can be easily switched on and off, by setting the value in the input XML file. 
 
-\begin{itemize} %Should have used a description list for this.
-\item \textbf{Snap to corresponding position}: When this is enabled, and a fragment is playing, the playhead skips to the same position in the next fragment that is clicked. If it is not enabled, every fragment is played from the start. 
-\item \textbf{Loop fragments}: Repeat current fragment when end is reached, until the `Stop audio' or `Submit' button is clicked. 
+\begin{itemize}[leftmargin=*]%Should have used a description list for this.
+\item \textbf{Snap to corresponding position}: When enabled and a fragment is playing, the playhead skips to the same position in the next fragment that is clicked. Otherwise, each fragment is played from the start. 
+\item \textbf{Loop fragments}: Repeat current fragment when end is reached, until the `Stop' or `Submit' button is clicked. 
 \item \textbf{Comments}: Displays a separate comment box for each fragment in the page.
-\item \textbf{General comment}: One comment box, additional to the individual comment boxes, to comment on the test or a feature that some or all of the fragments share. 
-\item \textbf{Resampling}: When this is enabled, tracks are resampled to match the subject's system's sample rate (a default feature of the Web Audio API). When it is not, an error is shown when the system does not match the requested sample rate. 
+\item \textbf{General comment}: Create additional comment boxes to the fragment comment boxes, with a custom question and various input formats such as checkbox or radio.
+\item \textbf{Resampling}: When this is enabled, fragments are resampled to match the subject's system's sample rate (a default feature of the Web Audio API). When it is not, an error is shown when the system does not match the requested sample rate. 
 \item \textbf{Randomise page order}: Randomises the order in which different `pages' are presented. % are we calling this 'pages'?
-\item \textbf{Randomise fragment order}: Randomises the order and numbering of the markers and comment boxes corresponding to the fragments. This permutation is stored as well, to be able to interpret references to the numbers in the comments (such as `this is much [brighter] then 4'). 
-\item \textbf{Require playback}: Require that each fragment has been played at least once, if not in full. 
-\item \textbf{Require full playback}: If `Require playback' is active, require that each fragment has been played in full. 
+\item \textbf{Randomise fragment order}: Randomises the order and numbering of the markers and comment boxes corresponding to the fragments. Fragments are referenced to their given ID so referencing is possible (such as `this is much brighter than fragment 4'). 
+\item \textbf{Require (full) playback}: Require that each fragment has been played at least once, partly or fully. 
 \item \textbf{Require moving}: Require that each marker is moved (dragged) at least once. 
-\item \textbf{Require comments}: This option allows requiring the subject to require a comment for each track. 
-\item \textbf{Repeat test}: Number of times each page in the test should be repeated (none by default), to allow familiarisation with the content and experiment, and to investigate consistency of user and variability due to familiarity. In the setup, each 'page' can be given a repeat count. These are all gathered before shuffling the order so repeated tests are not back-to-back if possible.
+\item \textbf{Require comments}: Require the subject to write a comment for each fragment. 
+\item \textbf{Repeat test}: Number of times each page in the test should be repeated (none by default), to allow familiarisation with the content and experiment, and to investigate consistency of user and variability due to familiarity. These are all gathered before shuffling the order so repeated tests are not back-to-back if possible.
 \item \textbf{Returning to previous pages}: Indicates whether it is possible to go back to a previous `page' in the test. 
 \item \textbf{Lowest rating below [value]}: To enforce a certain use of the rating scale, it can be required to rate at least one sample below a specified value. 
 \item \textbf{Highest rating above [value]}: To enforce a certain use of the rating scale, it can be required to rate at least one sample above a specified value. 
 \item \textbf{Reference}: Allows for a separate sample (outside of the axis) to be the `reference', which the subject can play back during the test to help with the task at hand \cite{mushra}. 
-\item \textbf{Hidden reference}: Whether or not an explicit `reference' is provided, the `hidden reference' should be rated above a certain value \cite{mushra} - this can be enforced. 
-\item \textbf{Hidden anchor}: The `hidden anchor' should be rated lower than a certain value \cite{mushra} - this can be enforced. 
+\item \textbf{Hidden reference/anchor}: Whether or not an explicit `reference' is provided, the `hidden reference' should be rated above a certain value \cite{mushra} - this can be enforced. 
+Similarly, a `hidden anchor' should be rated lower than a certain value \cite{mushra}. 
 \item \textbf{Show scrub bar}: Display a playhead on a scrub bar to show the position in the current fragment.
 %\item \textbf{Drag playhead}: If scrub bar is visible, allow dragging to move back or forward in a fragment. 
 \end{itemize}
@@ -327,20 +398,55 @@
 
 \subsection{Results}
 
-The results file is dynamically generated by the interface upon clicking the `Submit' button. This also executes checks, depending on the setup file, to ensure that all tracks have been played back, rated and commented on. The XML output returned contains a node per audioObject and contains both the corresponding marker's position and any comments written in the associated comment box. The rating returned is normalised to be a value between 0 and 1, normalising the pixel representation of different browser windows. An example output file is presented in Figure~\ref{fig:xmlOut}.
+The results file is dynamically generated by the interface upon clicking the `Submit' button. This also executes checks, depending on the setup file, to ensure that all fragments have been played back, rated and commented on. The XML output returned contains a node per fragment and contains both the corresponding marker's position and any comments written in the associated comment box. The rating returned is normalised to be a value between 0 and 1, normalising the pixel representation of different browser windows. The results also contain information collected by any defined pre/post questions. An excerpt of an output file is presented below detailing the data collected for a single audioElement.
 
-\begin{figure}[ht]
-\begin{center}
-\includegraphics[width=0.5\textwidth]{XMLOutput2.png}
-\caption{An example output XML file}
-\label{fig:xmlOut}
-\end{center}
-\end{figure}
+\scriptsize
+\lstset{language=XML}
 
-The results also contain information collected by any defined pre/post questions. These are referenced against the setup XML by using the same ID so readable responses can be obtained. Taking from the earlier example of setting up a pre-test question, an example response can be seen in Figure \ref{fig:xmlOut}.
+\begin{lstlisting}
+<browserevaluationresult>
+	<datetime>
+		<date year="2015" month="5" day="28">2015/5/28</date>
+		<time hour="13" minute="19" secs="17">13:19:17</time>
+	</datetime>
+	<pretest>
+		<comment id="location">Control Room</comment>
+	</pretest>
+	<audioholder>
+		<pretest></pretest>
+		<posttest>
+			<comment id="songGenre">Pop</comment>
+		</posttest>
+		<metric>
+			<metricresult id="testTime">813.32</metricresult>
+		</metric>
+		<audioelement id="elem1">
+			<comment>
+				<question>Comment on fragment 1</question>
+				<response>Good, but vocals too quiet.</response>
+			</comment>
+			<value>0.639010989010989</value>
+			<metric>
+				<metricresult id="elementTimer">111.05</metricresult>
+				<metricresult id="elementTrackerFull">
+					<timepos id="0">
+						<time>61.60</time>
+						<position>0.6390</position>
+					</timepos>
+				</metricresult>
+				<metricresult id="elementInitialPosition">0.6571</metricresult>
+				<metricresult id="elementFlagListenedTo">true</metricresult>
+			</metric>
+		</audioelement>
+	</audioHolder>
+</browserevaluationresult>
 
-Each page of testing is returned with the results of the entire page included in the structure. One `audioElement' node is created per audio fragment per page, along with its ID. This includes several child nodes including the rating between 0 and 1, the comment, and any other collected metrics including how long the element was listened for, the initial position, boolean flags if the element was listened to, if the element was moved and if the element comment box had any comment. Furthermore, each user action (manipulation of any interface element, such as playback or moving a marker) can be logged along with a the corresponding time code.
-We also store session data such as the browser the tool was used in. 
+\end{lstlisting}
+
+\normalsize
+\vspace{-.5em}
+Each page of testing is returned with the results of the entire page included in the structure. One \texttt{audioelement} node is created per audio fragment per page, along with its ID. This includes several child nodes including the rating between 0 and 1, the comment, and any other collected metrics including how long the element was listened for, the initial position, and boolean flags showing if the element was listened to, moved and commented on. Furthermore, each user action (manipulation of any interface element, such as playback or moving a marker) can be logged along with a the corresponding time code.
+We also store session data such as the time the test took place and the duration of the test.
 We provide the option to store the results locally, and/or to have them sent to a server. 
 
 %Here is an example of the set up XML and the results XML: % perhaps best to refer to each XML after each section (set up <> results)
@@ -371,13 +477,17 @@
 %</metric> \\
 %</audioelement>}
 
-The parent tag \texttt{audioelement} holds the ID of the element passed in from the setup document. The first child element is \texttt{comment} and holds both the question shown and the response from the comment box inside. 
-The child element \texttt{value} holds the normalised ranking value. Next comes the metric node structure, with one metric result node per metric event collected. The id of the node identifies the type of data it contains. For example, the first holds the id \textit{elementTimer} and the data contained represents how long, in seconds, the audio element was listened to. There is one \texttt{audioelement} tag per audio element on each test page. 
-
 % BRECHT: scripts
 
-Python scripts are included to easily store ratings and comments in a CSV file, and to display graphs of numerical ratings or the test's timeline. 
-Visualisation of plots requires the free matplotlib library. 
+\begin{figure}[htpb]
+\centering
+\includegraphics[width=.45\textwidth]{boxplot.png}
+\caption{An example boxplot showing ratings by different subjects on fragments labeled `A' through `G'. }
+\label{fig:boxplot}
+\end{figure}
+
+Python scripts are included to easily store ratings and comments in a CSV file, and to display graphs of numerical ratings (see Figure \ref{fig:boxplot}) or visualise the test's timeline. 
+Visualisation of plots requires the free matplotlib library\footnote{http://matplotlib.org}. 
 
 
 \section{Conclusions and future work}\label{sec:conclusions}
@@ -387,7 +497,7 @@
 The purpose of this paper is to outline the design of this tool, to describe our implementation using basic HTML5 functionality, and to discuss design challenges and limitations of our approach. This tool differentiates itself from other perceptual audio tools by enabling web technologies for multiple participants to perform the test without the need for proprietary software such as MATLAB. The tool also allows for any interface to be built using HTML5 elements to create a variety of dynamic, multiple-stimulus listening test interfaces. It enables quick setup of simple tests with the ability to manage complex tests through a single file. Finally it uses the XML document format to store the results allowing for processing and analysis of results in various third party software such as MATLAB or Python.
 
 % future work
-Further work may include the development of other common test designs, such as MUSHRA \cite{mushra}, 2D valence and arousal/activity \cite{ratingeerola2009prediction}, and others. We will add functionality to assist with setting up large-scale tests with remote subjects, so this becomes straightforward and intuitive. 
+Further work may include the development of other common test designs, such as MUSHRA \cite{mushra}, 2D valence and arousal/activity \cite{eerola2009prediction}, and others. We will add functionality to assist with setting up large-scale tests with remote subjects, so this becomes straightforward and intuitive. 
 In addition, we will keep on improving and expanding the tool, and highly welcome feedback and contributions from the community. 
 
 The source code of this tool can be found on \\ \texttt{code.soundsoftware.ac.uk/projects/}\\ \texttt{webaudioevaluationtool}. 

Binary file docs/SMC15/timeline.png has changed

--- a/index.html	Sun Jun 28 09:52:47 2015 +0100
+++ b/index.html	Mon Jun 29 19:04:40 2015 +0100
@@ -8,7 +8,7 @@
 		Remove this if you use the .htaccess -->
 		<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
 
-		<title>apeTool</title>
+		<title>Web Audio Evaluation Tool</title>
 		<meta name="description" content="" />
 		<meta name="author" content="" />
 		
@@ -25,7 +25,7 @@
 		</script>
 		<!-- Uncomment the following script for automatic loading of projects -->
 		<script>
-			url = 'example_eval/project.xml'; //Project XML document location
+			url = '/pseudo.xml'; //Project XML document location
 			loadProjectSpec(url);
 		</script>
 		

--- a/python2.py	Sun Jun 28 09:52:47 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-import BaseHTTPServer
-from os import walk
-from os import path
-import urllib2
-import pickle
-import datetime
-
-curSaveIndex = 0;
-curFileName = 'test-0.xml'
-while(path.isfile('saves/'+curFileName)):
-	curSaveIndex += 1;
-	curFileName = 'test-'+str(curSaveIndex)+'.xml'
-
-print curFileName
-
-def send404(s):
-	s.send_response(404)
-	s.send_header("Content-type", "text/html")
-	s.end_headers()
-	
-def processFile(s):
-	s.path = s.path[1:len(s.path)]
-	st = s.path.rsplit(',')
-	lenSt = len(st)
-	fmt = st[lenSt-1].rsplit('.')
-	size = path.getsize(urllib2.unquote(s.path))
-	fileDump = open(urllib2.unquote(s.path))
-	s.send_response(200)
-	
-	if (fmt[1] == 'html'):
-		s.send_header("Content-type", 'text/html')
-	elif (fmt[1] == 'css'):
-		s.send_header("Content-type", 'text/css')
-	elif (fmt[1] == 'js'):
-		s.send_header("Content-type", 'application/javascript')
-	else:
-		s.send_header("Content-type", 'application/octet-stream')
-	s.send_header("Content-Length", size)
-	s.end_headers()
-	s.wfile.write(fileDump.read())
-	fileDump.close()
-	
-def saveFile(self):
-	global curFileName
-	global curSaveIndex
-	varLen = int(self.headers['Content-Length'])
-	postVars = self.rfile.read(varLen)
-	print curFileName
-	file = open('saves/'+curFileName,'w')
-	curSaveIndex += 1;
-	curFileName = 'test-'+str(curSaveIndex)+'.xml'
-	print curFileName
-	file.write(postVars)
-	file.close()
-	self.send_response(200)
-	self.send_header("Content-type", "text/xml")
-	self.end_headers()
-	self.wfile.write('<response><state>OK</state><file>saves/'+curFileName+'</file></response>')
-
-class MyHandler(BaseHTTPServer.BaseHTTPRequestHandler):
-	def do_HEAD(s):
-			s.send_response(200)
-			s.send_header("Content-type", "text/html")
-			s.end_headers()
-	def do_GET(request):
-		if(request.client_address[0] == "127.0.0.1"):
-			if (request.path == "/favicon.ico"):
-				send404(request)
-			else:
-				if (request.path == '/'):
-					request.path = '/index.html'
-				processFile(request)
-		else:
-			send404(request)
-	def do_POST(request):
-		if(request.client_address[0] == "127.0.0.1"):
-			if (request.path == "/save"):
-				saveFile(request)
-		else:
-			send404(request)
-
-def run(server_class=BaseHTTPServer.HTTPServer,
-        handler_class=MyHandler):
-    server_address = ('', 8000)
-    httpd = server_class(server_address, handler_class)
-    httpd.serve_forever()
-
-run()
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pythonServer-legacy.py	Mon Jun 29 19:04:40 2015 +0100
@@ -0,0 +1,11 @@
+import SimpleHTTPServer
+import SocketServer
+
+PORT = 8080
+
+Handler = SimpleHTTPServer.SimpleHTTPRequestHandler
+
+httpd = SocketServer.TCPServer(("", PORT), Handler)
+
+print "serving at port", PORT
+httpd.serve_forever()

--- a/pythonServer.py	Sun Jun 28 09:52:47 2015 +0100
+++ b/pythonServer.py	Mon Jun 29 19:04:40 2015 +0100
@@ -1,11 +1,106 @@
-import SimpleHTTPServer
-import SocketServer
+import BaseHTTPServer
+from os import walk
+from os import path
+from os import listdir
+import urllib2
+import pickle
+import datetime
 
-PORT = 8080
+PSEUDO_PATH = 'example_eval/'
+pseudo_files = []
+for filename in listdir(PSEUDO_PATH):
+    if filename.endswith('.xml'):
+        pseudo_files.append(filename)
 
-Handler = SimpleHTTPServer.SimpleHTTPRequestHandler
+curSaveIndex = 0;
+curFileName = 'test-0.xml'
+while(path.isfile('saves/'+curFileName)):
+	curSaveIndex += 1;
+	curFileName = 'test-'+str(curSaveIndex)+'.xml'
 
-httpd = SocketServer.TCPServer(("", PORT), Handler)
+print "Next save - " + curFileName
+pseudo_index = curSaveIndex % len(pseudo_files)
+print "Next test - " + pseudo_files[pseudo_index]
 
-print "serving at port", PORT
-httpd.serve_forever()
+def send404(s):
+	s.send_response(404)
+	s.send_header("Content-type", "text/html")
+	s.end_headers()
+	
+def processFile(s):
+	s.path = s.path[1:len(s.path)]
+	st = s.path.rsplit(',')
+	lenSt = len(st)
+	fmt = st[lenSt-1].rsplit('.')
+	size = path.getsize(urllib2.unquote(s.path))
+	fileDump = open(urllib2.unquote(s.path))
+	s.send_response(200)
+	
+	if (fmt[1] == 'html'):
+		s.send_header("Content-type", 'text/html')
+	elif (fmt[1] == 'css'):
+		s.send_header("Content-type", 'text/css')
+	elif (fmt[1] == 'js'):
+		s.send_header("Content-type", 'application/javascript')
+	else:
+		s.send_header("Content-type", 'application/octet-stream')
+	s.send_header("Content-Length", size)
+	s.end_headers()
+	s.wfile.write(fileDump.read())
+	fileDump.close()
+	
+def saveFile(self):
+	global curFileName
+	global curSaveIndex
+	varLen = int(self.headers['Content-Length'])
+	postVars = self.rfile.read(varLen)
+	print curFileName
+	file = open('saves/'+curFileName,'w')
+	curSaveIndex += 1;
+	curFileName = 'test-'+str(curSaveIndex)+'.xml'
+	print curFileName
+	file.write(postVars)
+	file.close()
+	self.send_response(200)
+	self.send_header("Content-type", "text/xml")
+	self.end_headers()
+	self.wfile.write('<response><state>OK</state><file>saves/'+curFileName+'</file></response>')
+
+class MyHandler(BaseHTTPServer.BaseHTTPRequestHandler):
+	def do_HEAD(s):
+		s.send_response(200)
+		s.send_header("Content-type", "text/html")
+		s.end_headers()
+	def do_GET(request):
+		global pseudo_index
+		global pseudo_files
+		global PSEUDO_PATH
+		if(request.client_address[0] == "127.0.0.1"):
+			if (request.path == "/favicon.ico"):
+				send404(request)
+			else:
+				if (request.path == '/'):
+					request.path = '/index.html'
+				elif (request.path == '/pseudo.xml'):
+					request.path = '/'+PSEUDO_PATH + pseudo_files[pseudo_index]
+					print request.path
+					pseudo_index += 1
+					pseudo_index %= len(pseudo_files)
+				processFile(request)
+		else:
+			send404(request)
+
+	def do_POST(request):
+		if(request.client_address[0] == "127.0.0.1"):
+			if (request.path == "/save"):
+				saveFile(request)
+		else:
+			send404(request)
+
+def run(server_class=BaseHTTPServer.HTTPServer,
+        handler_class=MyHandler):
+    server_address = ('', 8000)
+    httpd = server_class(server_address, handler_class)
+    httpd.serve_forever()
+
+run()
\ No newline at end of file

--- a/saves/read.txt	Sun Jun 28 09:52:47 2015 +0100
+++ b/saves/read.txt	Mon Jun 29 19:04:40 2015 +0100
@@ -1,2 +1,2 @@
-This folder is where the python2.py server will save the received test results
+This folder is where the pythonServer.py server will save the received test results
 Files will return as test-#.xml where # is the number they were received!

--- a/scripts/comment_parser.py	Sun Jun 28 09:52:47 2015 +0100
+++ b/scripts/comment_parser.py	Mon Jun 29 19:04:40 2015 +0100
@@ -1,11 +1,17 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
 import xml.etree.ElementTree as ET
 import os
 import csv
 
+# XML results files location (modify as needed):
+folder_name = "../saves"    # Looks in 'saves/' folder from 'scripts/' folder
+
 # get every XML file in folder
-for file in os.listdir("."): # You have to put this script in folder where output XML files are.
+for file in os.listdir(folder_name): 
     if file.endswith(".xml"):
-        tree = ET.parse(file)
+        tree = ET.parse(folder_name + '/' + file)
         root = tree.getroot()
 
         # get list of all page names
@@ -16,31 +22,34 @@
                 break
 
             # create folder [page_name] if not yet created
-            if not os.path.exists(page_name):
-                os.makedirs(page_name)
+            if not os.path.exists(folder_name + "/" + page_name):
+                os.makedirs(folder_name + "/" + page_name)
 
             # for page [page_name], print comments related to fragment [id]
-            for audioelement in root.findall("*/[@id='"+page_name+"']/audioelement"):
+            for audioelement in audioholder.findall("./audioelement"):
                 if audioelement is not None: # Check it exists
                     audio_id = str(audioelement.get('id'))
+                    
+                    csv_name = folder_name +'/' + page_name+'/'+page_name+'-comments-'+audio_id+'.csv'
 
-                    # append to file [page_name]/[page_name]-comments-[id].csv
-                    with open(page_name+'/'+page_name+'-comments-'+audio_id+'.csv', 'a') as csvfile:
-                        writer = csv.writer(csvfile, delimiter=',')
-                        commentstr = root.find("*/[@id='"
-                                               + page_name
-                                               + "']/audioelement/[@id='"
-                                               + audio_id
-                                               + "']/comment/response").text
+                    # append (!) to file [page_name]/[page_name]-comments-[id].csv
+                    with open(csv_name, 'a') as csvfile:
+                        writer = csv.writer(csvfile, 
+                                            delimiter=',', 
+                                            dialect="excel",
+                                            quoting=csv.QUOTE_ALL)
+                        commentstr = audioelement.find("./comment/response").text
+                        
                         if commentstr is None:
-                            writer.writerow([''])
-                        else:
-                            writer.writerow([commentstr.encode("utf-8")])
-                        #TODO Comma doesn't act as delimiter now!
-                        # (when adding more than just a comment per line):
-                        # writer.writerow([file + ',' + commentstr.encode("utf-8")])
+                           commentstr = '';
+                            
+                        # anonymous comments:
+                        #writer.writerow([commentstr.encode("utf-8")]) 
+                        # comments with (file) name:
+                        writer.writerow([file[:-4]] + [commentstr.encode("utf-8")]) 
 
-                        #TODO Replace 'new line' with something else?
-
-                        #TODO 'Append' means duplicate entries if run several times...
-
+                        #TODO Replace 'new line' in comment with something else?
+                        
+# PRO TIP: Change from csv to txt by running this in bash: 
+# $ cd folder_where_csvs_are/
+# $ for i in *.csv; do mv "$i" "${i/.csv}".txt; done

--- a/scripts/score_boxplot.py	Sun Jun 28 09:52:47 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-import sys
-import os
-import csv
-import matplotlib.pyplot as plt
-import numpy as np
-
-rating_folder = 'ratings/' # folder with rating csv files
-show_individual = 'frank'
-
-# get every csv file in folder
-for file in os.listdir(rating_folder): # You have to put this in folder where rating csv files are.
-    if file.endswith(".csv"):
-        page_name = file[:-4] # file name (without extension) is page ID
-
-        # get header
-        with open(rating_folder+file, 'r') as readfile: # read this csv file
-            filereader = csv.reader(readfile, delimiter=',')
-            headerrow = filereader.next() # use headerrow as X-axis
-            headerrow = headerrow[1:]
-
-        # read ratings into matrix
-        ratings = np.loadtxt(open(rating_folder+file,"rb"),
-                            delimiter=",",
-                            skiprows=1,
-                            usecols=range(1,len(headerrow)+1)
-                            )
-
-        # draw boxplot
-        plt.boxplot(ratings)
-
-        # add rating of individual(s)
-        with open(rating_folder+file, 'r') as readfile: # read this csv file
-            filereader = csv.reader(readfile, delimiter=',')
-            headerrow = filereader.next() # use headerrow as X-axis
-            headerrow = headerrow[1:]
-            markerlist = ["x", ".", "o", "*", "+", "v", ">", "<", "8", "s", "p"]
-            increment = 0
-            linehandles = []
-            legendnames = []
-            for row in filereader:
-                subject_id = row[0][:-4]
-                if subject_id in show_individual:
-                    plothandle, = plt.plot(range(1,len(row)), # x-values
-                             row[1:], # y-values: csv values except subject name
-                             color='k',
-                             marker=markerlist[increment%len(markerlist)],
-                             markersize=10,
-                             linestyle='None',
-                             label=subject_id
-                            )
-                    increment += 1 # increase counter
-                    linehandles.append(plothandle)
-                    legendnames.append(subject_id)
-                    plt.legend(linehandles, legendnames,
-                           loc='upper right',
-                           bbox_to_anchor=(1.1, 1), borderaxespad=0.)
-
-
-        plt.xlabel('Fragment')
-        plt.title('Box plot '+page_name)
-        plt.xlim(0, len(headerrow)+1) # only show relevant region, leave space left & right)
-        plt.xticks(range(1, len(headerrow)+1), headerrow) # show fragment names
-
-        plt.ylabel('Rating')
-        plt.ylim(0,1)
-
-        #plt.show() # show plot
-        #exit()
-
-        plt.savefig(rating_folder+page_name+"-box.png")
-        plt.close()

--- a/scripts/score_individual.py	Sun Jun 28 09:52:47 2015 +0100
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-import sys
-import os
-import csv
-import matplotlib.pyplot as plt
-
-rating_folder = 'ratings/' # folder with rating csv files
-
-colormap = ['b', 'r', 'g', 'c', 'm', 'y', 'k'] # colormap for to cycle through
-markerlist = ["x", ".", "o", "*", "+", "v", ">", "<", "8", "s", "p"]
-
-show_legend = False
-
-# get every csv file in folder
-for file in os.listdir(rating_folder):
-    if file.endswith(".csv"):
-        
-        page_name = file[:-4] # file name (without extension) is page ID
-
-        with open(rating_folder+file, 'r') as readfile: # read this csv file
-            filereader = csv.reader(readfile, delimiter=',')
-            headerrow = filereader.next() # use headerrow as X-axis
-            headerrow = headerrow[1:]
-
-
-            increment = 0
-            linehandles = []
-            legendnames = []
-            for row in filereader:
-                subject_id = row[0][:-4]
-                plothandle, = plt.plot(range(1,len(row)), # x-values
-                         row[1:], # y-values: csv values except subject name
-                         color=colormap[increment%len(colormap)],
-                         marker=markerlist[increment%len(markerlist)],
-                         markersize=10,
-                         linestyle='None',
-                         label=subject_id
-                        )
-                increment += 1 # increase counter
-                linehandles.append(plothandle)
-                legendnames.append(subject_id.decode("utf-8")) # avoid decoding problems
-
-
-            plt.xlabel('Fragment')
-            plt.title('Individual ratings '+page_name)
-            plt.xlim(0, len(headerrow)+1) # only show relevant region, leave space left & right)
-            plt.xticks(range(1, len(headerrow)+1), headerrow) # show fragment names
-
-            plt.ylabel('Rating')
-            plt.ylim(0,1)
-
-            if show_legend:
-                plt.legend(linehandles, legendnames,
-                           loc='upper right',
-                           bbox_to_anchor=(1.1, 1),
-                           borderaxespad=0.,
-                           numpoints=1 # remove extra marker
-                           )
-
-            #TODO Put legend outside of box
-
-            #plt.show() # show plot
-            #exit()
-            
-            plt.savefig(rating_folder+page_name+"-ind.png")
-            plt.close()

--- a/scripts/score_parser.py	Sun Jun 28 09:52:47 2015 +0100
+++ b/scripts/score_parser.py	Mon Jun 29 19:04:40 2015 +0100
@@ -1,38 +1,42 @@
+#!/usr/bin/python
+
 import xml.etree.ElementTree as ET
 import os
 import csv
 
 #TODO Remove DEBUG statements
 
+# XML results files location (modify as needed):
+folder_name = "../saves"    # Looks in 'saves/' folder from 'scripts/' folder
+
 # get every XML file in folder
-for file in os.listdir("."): # You have to put this in folder where output XML files are.
+for file in os.listdir(folder_name):
     if file.endswith(".xml"):
-        tree = ET.parse(file)
+        tree = ET.parse(folder_name + '/' + file)
         root = tree.getroot()
-        #print ["DEBUG Reading " + file + "..."]
+        #print "DEBUG Reading " + file + "..."
 
         # get subject ID from XML file
-        subject_id = file # file name as subject ID
+        subject_id = file[:-4] # file name (without extension) as subject ID
 
         # get list of all pages this subject evaluated
         for audioholder in root.findall("./audioholder"):    # iterate over pages
             page_name = audioholder.get('id') # get page name
-            #print ["DEBUG    page " + page_name]
-            
+                       
             if page_name is None: # ignore 'empty' audio_holders
                 break
 
-            file_name = 'ratings/'+page_name+'-ratings.csv' # score file name
+            file_name = folder_name+'/ratings/'+page_name+'-ratings.csv' # score file name
 
             # create folder 'ratings if not yet created
-            if not os.path.exists('ratings'):
-                os.makedirs('ratings')
+            if not os.path.exists(folder_name + '/ratings'):
+                os.makedirs(folder_name + '/ratings')
 
             # header: fragment IDs in 'alphabetical' order
             # go to fragment column, or create new column if it doesn't exist yet
 
             # get array of audio elements and number of audio elements
-            audiolist = root.findall("*/[@id='"+page_name+"']/audioelement")
+            audiolist = audioholder.findall("./audioelement")
             n_fragments = len(audiolist)
 
             # get alphabetical array of fragment IDs from this subject's XML
@@ -43,28 +47,31 @@
 
             # if file exists, get header and add 'new' fragments
             if os.path.isfile(file_name):
-                #print ["DEBUG file " + file_name + " already exists - reading header"]
+                #print "DEBUG file " + file_name + " already exists - reading header"
                 with open(file_name, 'r') as readfile:
                     filereader = csv.reader(readfile, delimiter=',')
                     headerrow = filereader.next()
-                    #headerrow = headerrow[1:] # remove first column (empty)
 
-                    # Which of the fragmentes are in fragmentnamelist but not in headerrow?
-                    newfragments = list(set(fragmentnamelist)-set(headerrow))
-                    newfragments = sorted(newfragments) # new fragments in alphabetical order
-                    # If not empty, read file and rewrite adding extra columns
-                    if newfragments: # if not empty
-                        print ["DEBUG New fragments found: " + str(newfragments)]
-                        with open('temp.csv', 'w') as writefile:
-                            filewriter = csv.writer(writefile, delimiter=',')
-                            filewriter.writerow(headerrow + newfragments) # write new header
+                # Which of the fragmentes are in fragmentnamelist but not in headerrow?
+                newfragments = list(set(fragmentnamelist)-set(headerrow))
+                newfragments = sorted(newfragments) # new fragments in alphabetical order
+                # If not empty, read file and rewrite adding extra columns
+                if newfragments: # if not empty
+                    #print "DEBUG New fragments found: " + str(newfragments)
+                    with open('temp.csv', 'w') as writefile:
+                        filewriter = csv.writer(writefile, delimiter=',')
+                        filewriter.writerow(headerrow + newfragments) # write new header
+                        #print "        "+str(headerrow + newfragments) # DEBUG
+                        with open(file_name, 'r') as readfile:
+                            filereader = csv.reader(readfile, delimiter=',')
+                            filereader.next() # skip header
                             for row in filereader: # rewrite row plus empty cells for every new fragment name
-                                #print ["DEBUG Old row: " + str(row)]
+                                #print "            Old row: " + str(row) # DEBUG
                                 filewriter.writerow(row + ['']*len(newfragments))
-                                #print ["DEBUG New row: " + str(row + ['']*len(newfragments))]
-                        os.rename('temp.csv', file_name) # replace old file with temp file
-                        headerrow = headerrow + newfragments
-                        print ["DEBUG New header row: " + str(headerrow)]
+                                #print "            New row: " + str(row + ['']*len(newfragments)) # DEBUG
+                    os.rename('temp.csv', file_name) # replace old file with temp file
+                    headerrow = headerrow + newfragments
+                    #print "DEBUG New header row: " + str(headerrow)
 
             # if not, create file and make header
             else:
@@ -85,9 +92,7 @@
 
             # get scores related to fragment [id]
             for fragmentname in headerrow[1:]: # iterate over fragments in header (skip first empty column)
-                elementvalue = root.find("*/[@id='"
-                                       + page_name
-                                       + "']/audioelement/[@id='"
+                elementvalue = audioholder.find("./audioelement/[@id='"
                                        + fragmentname
                                        + "']/value")
                 if hasattr(elementvalue, 'text'): # if rating for this fragment exists
@@ -96,5 +101,6 @@
                     ratingrow.append('') # append empty cell
 
             # write row: [subject ID, rating fragment ID 1, ..., rating fragment ID M]
-            filewriter.writerow(ratingrow)
+            if any(ratingrow[1:]): # append to file if row non-empty (except subject name)
+                filewriter.writerow(ratingrow)
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/score_plot.py	Mon Jun 29 19:04:40 2015 +0100
@@ -0,0 +1,150 @@
+#!/usr/bin/python
+
+import sys
+import os
+import csv
+import matplotlib.pyplot as plt
+import numpy as np
+import scipy as sp
+import scipy.stats
+
+# CONFIGURATION
+
+# Which type(s) of plot do you want? 
+enable_boxplot    = False     # show box plot
+enable_confidence = True      # show confidence interval
+confidence        = 0.90      # confidence value (for confidence interval plot)
+enable_individual = True      # show all individual ratings
+show_individual   = []        # show specific individuals
+show_legend       = False     # show names of individuals
+#TODO: Merge, implement this functionality
+#TODO: Control by CLI arguments (plot types, save and/or show, ...) 
+
+# Enter folder where rating CSV files are (generated with score_parser.py or same format).
+rating_folder = '../saves/ratings/' # folder with rating csv files
+
+# Font settings
+font = {'weight' : 'bold',
+        'size'   : 10}
+plt.rc('font', **font)
+
+
+# CODE
+
+# get every csv file in folder
+for file in os.listdir(rating_folder): # You have to put this in folder where rating csv files are.
+    if file.endswith(".csv"):
+        page_name = file[:-4] # file name (without extension) is page ID
+
+        # get header
+        with open(rating_folder+file, 'rb') as readfile: # read this csv file
+            filereader = csv.reader(readfile, delimiter=',')
+            headerrow = filereader.next() # use headerrow as X-axis
+            headerrow = headerrow[1:]
+
+        # read ratings into matrix
+#         ratings = np.loadtxt(open(rating_folder+file,"rb"),
+#                             delimiter=",",
+#                             skiprows=1,
+#                             usecols=range(1,len(headerrow)+1)
+#                             )
+            ratings = np.genfromtxt(readfile,
+                                   delimiter=",",
+                                   #skip_header = 1,
+                                   converters = {3: lambda s: float(s or 'Nan')},
+                                   usecols=range(1,len(headerrow)+1)
+                                   )
+        
+        # assert at least 2 subjects (move on to next file if violated)
+        if ratings.shape[1]<2:
+            print "WARNING: Just one subject for " + page_name + ". Moving on to next file."
+            break
+
+        # BOXPLOT
+        if enable_boxplot:
+            plt.boxplot(ratings)
+            
+        # CONFIDENCE INTERVAL
+        if enable_confidence:
+            iterator = 0
+            for column in ratings.T: # iterate over transposed matrix
+                # remove all 'Nan's from column
+                column = column[~np.isnan(column)]
+            
+                # get number of non-Nan ratings (= #subjects)
+                n = column.size
+        
+                # get mean
+                mean_rating = np.mean(column)
+        
+                # get errors
+                err = scipy.stats.sem(column)* sp.stats.t._ppf((1+confidence)/2., n-1)
+        
+                # draw plot
+                plt.errorbar(iterator+1, 
+                            mean_rating, 
+                            yerr=err,
+                            marker="x",
+                            color ="k",
+                            markersize=12,
+                            linestyle='None')
+                            
+                iterator += 1 # increase counter
+    
+    
+        # INDIVIDUAL PLOT
+        if enable_individual or show_individual:
+            # marker list and color map to cycle through
+            markerlist = ["x", ".", "o", "*", "+", "v", ">", "<", "8", "s", "p"]
+            colormap = ['b', 'r', 'g', 'c', 'm', 'y', 'k'] 
+            increment = 0
+            linehandles = []
+            legendnames = []
+            with open(rating_folder+file, 'rb') as readfile: # read this csv file
+                filereader = csv.reader(readfile, delimiter=',')
+                headerrow = filereader.next() # use headerrow as X-axis
+                headerrow = headerrow[1:]
+                for row in filereader:
+                    subject_id = row[0][:-4] # read from beginning of line
+                    # assume plotting all individuals if no individual(s) specified
+                    if not show_individual or subject_id in show_individual:
+                        plothandle, = plt.plot(range(1,len(row)), # x-values
+                                 ratings[increment,:],#row[1:], # y-values: csv values except subject name
+                                 color=colormap[increment%len(colormap)],
+                                 marker=markerlist[increment%len(markerlist)],
+                                 markersize=10,
+                                 linestyle='None',
+                                 label=subject_id
+                                )
+                        linehandles.append(plothandle)
+                        legendnames.append(subject_id)
+                        if show_legend:
+                            plt.legend(linehandles, legendnames,
+                                       loc='upper right',
+                                       bbox_to_anchor=(1.1, 1),
+                                       borderaxespad=0.,
+                                       numpoints=1 # remove extra marker
+                                       )
+                    increment += 1 # increase counter
+
+        # TITLE, AXIS LABELS AND LIMITS
+        plt.title(page_name)
+        plt.xlabel('Fragment')
+        plt.xlim(0, len(headerrow)+1) # only show relevant region, leave space left & right)
+        plt.xticks(range(1, len(headerrow)+1), headerrow) # show fragment names
+        plt.ylabel('Rating')
+        plt.ylim(0,1)
+        
+        
+
+        # SHOW PLOT
+        #plt.show()
+        #exit()
+    
+        # SAVE PLOT
+        # automatically 
+        plot_type = ("-box" if enable_boxplot else "") + \
+                    ("-conf" if enable_confidence else "") + \
+                    ("-ind" if enable_individual else "")
+        plt.savefig(rating_folder+page_name+plot_type+".png")
+        plt.close()

--- a/scripts/timeline_view.py	Sun Jun 28 09:52:47 2015 +0100
+++ b/scripts/timeline_view.py	Mon Jun 29 19:04:40 2015 +0100
@@ -1,20 +1,36 @@
+#!/usr/bin/python
+
 import xml.etree.ElementTree as ET
 import os
 import matplotlib.pyplot as plt
 
-colormap = ['b', 'r', 'g', 'c', 'm', 'y', 'k'] # colormap for to cycle through
+# CONFIGURATION 
 
-timeline_folder = 'timelines/' # folder where to store timelines, e.g. 'timelines/'
+# XML results files location (modify as needed):
+folder_name = "../saves"    # Looks in 'saves/' folder from 'scripts/' folder
 
+# Folder where to store timelines
+timeline_folder = folder_name + '/timelines/'    # Stores in 'saves/timelines/'
+
+# Font settings
+font = {'weight' : 'bold',
+        'size'   : 16}
+plt.rc('font', **font)
+
+# Colormap for to cycle through
+colormap = ['b', 'r', 'g', 'c', 'm', 'y', 'k']
+
+
+# CODE
 
 # create timeline_folder if not yet created
 if not os.path.exists(timeline_folder):
     os.makedirs(timeline_folder)
 
 # get every XML file in folder
-for file in os.listdir("."): # You have to put this script in folder where output XML files are.
+for file in os.listdir(folder_name):
     if file.endswith(".xml"):
-        tree = ET.parse(file)
+        tree = ET.parse(folder_name + '/' + file)
         root = tree.getroot()
         subject_id = file[:-4] # drop '.xml'
         
@@ -28,7 +44,7 @@
                 break
 
             # SORT AUDIO ELEMENTS ALPHABETICALLY
-            audioelements = root.findall("*/[@id='"+page_name+"']/audioelement")
+            audioelements = audioholder.findall("./audioelement")
             
             data = []
             for elem in audioelements: # from http://effbot.org/zone/element-sort.htm
@@ -48,11 +64,7 @@
                     audioelements_names.append(audio_id)
                     
                     # for this audioelement, loop over all listen events
-                    listen_events = root.findall("*/[@id='"
-                                           + page_name
-                                           + "']/audioelement/[@id='"
-                                           + audio_id
-                                           + "']/metric/metricresult/[@name='elementListenTracker']/event")
+                    listen_events = audioelement.findall("./metric/metricresult/[@name='elementListenTracker']/event")
                     for event in listen_events:
                         # get testtime: start and stop
                         start_time = event.find('testtime').get('start')