Bachelor thesis - Department of Cybernetics

Bachelor thesis - Department of Cybernetics
CZECH TECHNICAL UNIVERSITY IN PRAGUE
Faculty of Electrical Engineering
Bachelor thesis
Michal Zeman
Application for Feature Extraction
from Eye Movement Signal Analysis
2013
Department of Cybernetics
Thesis supervisor: Ing. Martin Macaš, Ph.D.
Czech Technical University in Prague
Faculty of Electrical Engineering
Department of Cybernetics
BACHELOR P R O J E C T ASSIGNMENT
Student:
Michal
Zeman
Study programme:
Cybernetics and Robotics
Specialisation:
Robotics
Title of Bachelor Project: Application for Feature Extraction from Eye Movement Signal
Analysis
Guidelines:
1. Develop an application with GUI for automatic feature extraction from results of analysis
of eye movement signals.
The application will enable:
a. mass feature extraction for multiple analysis files
b. basic statistical analysis and visualization of features
c. simple extendibility in terms of additional feature extractors
2. Validate the application on provided analysis files
a. Apply the mass feature extraction
b. Compare the results with the sample results provided by the supervisor
Bibliography/Sources:
[1] Jakub Snopek: Metody analyzy zaznamu ocnich pohybu pfi cteni a v sekvencnich ulohach.
Diplomova prace, katedra kybernetiky, CVUT, 2003.
[2] Martin Macas: Dyslexia detection using artificial neural networks. Katedra kybernetiky,
CVUT, 2005.
Bachelor Project Supervisor: Ing. Martin Macas, Ph.D.
Valid until: the end of the winter semester of academic year 2013/2014
Head of Department
Dean
Prague, January 10, 2013
C e s k e vysoke uceni technicke v Praze
Fakulta elektrotechnicka
Katedra kybernetiky
ZADANI B A K A L A R S K E P R A C E
Student:
Michal
Z eman
Studijni program:
Kybernetika a robotika (bakalafsky)
Obor:
Robotika
Nazev tematu:
Apiikace pro extrakci pnznaku z analyz signalu ocnich pohybu
Pokyny pro vypracovani:
1. Vytvorte aplikaci s GUI pro automatickou extrakci pnznaku z vysledku analyz signalu ocnich
pohybu.
Apiikace bude umoznovat:
a. hromadnou extrakci pnznaku pro vice souboru analyz
b. zakladni statistickou analyzu a vizualizaci pnznaku
c. snadnou rozsifitelnost o daisi extraktory
2. Validujte aplikaci na souborech analyz dodanych vedoucim prace
a. Proved'te hromadnou extrakci pnznaku
b. Porovnejte s dodanym vzorovym vysledkem
Seznam odborne literatury:
[1] Jakub Snopek: Metody analyzy zaznamu ocnich pohybu pfi cteni a v sekvencnich ulohach.
Diplomova prace, katedra kybernetiky, CVUT, 2003.
[2] Martin Macas: Dyslexia detection using artificial neural networks. Katedra kybernetiky,
CVUT, 2005.
Vedouci bakalafske prace: Ing. Martin Macas, Ph.D.
Platnost zadani: do konce zimniho semestru 2013/2014
Prohlaseni
Prohlasuji, ze jsem pfedlozenou praci vypracoval samostatne a ze jsem uvedl veskere
pouzite informacni zdroje v souladu s Metodickym pokynem o dodrzovani etickych
principu pfi pfiprave vysokoskolskych zaverecnych praci.
VPraze
dne...2^.5..2:CM3
Acknowledgements
First and foremost, I would like to thank my supervisor Ing. Martin Macaš for many
valuable suggestions, moral support and productive conversations. My gratitude also goes
to Ing. Daniel Novák, who introduced me to Ing. Macaš. Finally, let me thank my whole
family for their great support and great patience.
Abstrakt
Hlavním cílem této práce bylo navrhnout aplikaci s grafickým uživatelským rozhraním pro
hromadnou extrakci příznaků z analýz signálů očních pohybů v prostředí Matlab a
struktury souborů příznakových extraktorů. Tato aplikace významně pomůže v budoucím
studiu očních pohybů. Pomocí videookulografické metody (VOG) byla naměřena data pro
otestování hromadné extrakce příznaků. Bylo vyhodnoceno celkem 15 záznamů
pocházejících z měření očních pohybů zdravých subjektů při řešení verbálních i
neverbálních sekvenčních úloh. Na tomto vzorku dat byla otestována funkčnost
automatické hromadné extrakce příznaků.
Abstract
The main goal if this work is to propose the application with graphic user interface for
mass feature extraction from eye movement signal analysis in Matlab environment and
structure of feature extractors files. This application will significantly help in future studies
of eye movements. Using the videooculography method (VOG) were measured the signal
data for mass feature extraction. In total signal data of 15 healthy subjects in dealing with
verbal and non-verbal sequential tasks were processed. On this data sample was tested the
functionality of automatic mass feature extraction.
Application for Feature Extraction
from Eye Movement Signal Analysis
CONTENTS
Contents
1
Introduction
1.1.
Main goals
2
1.2.
Motivation
2
1.3.
Recording of eye movements
3
1.4.
Signal analysis
4
1.4.1.
1.5.
6
1.5.2.
Numerosity based features
6
1.5.3.
Latency and distance based features
7
1.5.4.
Frequency based features
7
Classification
8
Implementation
9
Signal data
9
EMSA structure
9
2.2.
Feature extractors
12
2.3.
Graphical User Interface
12
2.3.1.
Output
14
Validation
3.1.
15
Feature extractors description
15
3.1.1.
Out of screen proportion (out_of_screen, out_of_screen2)
15
3.1.2.
Stimuli type (stimuli_type)
17
3.1.3.
Task time (task_time)
17
3.2.
Mass extraction
18
Conclusion
4.1.
A
Feature extraction
6
2.1.1.
4
5
Position based features
2.1.
3
Classification of eye movements
1.5.1.
1.6.
2
1
20
Future work
21
Eye Movements Feature Extraction Tool manual
A.1
Table of contents
22
23
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Application for Feature Extraction
from Eye Movement Signal Analysis
LIST OF TABLES
List of tables
Table 1 - This table shows different types of eye movements, their length in milliseconds,
amplitude and velocity (adapted from Holmqvist, 2011).
5
Table 2 - extractors
18
Table 3 - file_names
19
Table 4 - results
19
List of figures
Figure 1 - A block diagram of the proposed method, the part highlighted in yellow is
concerned with this bachelor thesis
Figure 2 - EMSA structure
Figure 3 - 33.4% of signal data are out of screen
Figure 4 - dots2
Figure 5 - Task time of different subjects
2
10
16
17
18
List of pictures
Picture 1 - I4Tracking measuring device
4
Picture 2 - EyeMove Toolbox
4
Picture 3 - Saccades and fixations during reading task (picture adapted from Rayner, 2007)
6
Picture 4 - Application window
13
Software
Matlab Version 2012b, The MathWorks, Inc.
I4Tracking, Medicton s.r.o.
EMSA toolbox
ii
1. INTRODUCTION
Application for Feature Extraction
from Eye Movement Signal Analysis
Chapter 1
1
Introduction
Introduction
Human eye is an extraordinary organ. The ability to see helped the development of
human and other species. In last few decades it happened to be not only our main tool to
see, but also a powerful tool in diagnose of serious human conditions. The measurement of
human eye movements in last few decades led to important discoveries about
psychological processes that occur during reading, visual search and scene perception.
There are several studies describing the relationship between eye movements and
genetic or developmental disorders such as dyslexia (Pavlidis, 1985; Biscaldi, 1998;
Macaš, 2005), sexual deviance, schizophrenia (O’Driscoll and Callahan, 2008) etc.
However these studies do not provide any clear unified conclusions. In a study of eye
movements is a lot of space for additional research.
This work focus on providing user application that can help in further research of eye
movements using the methods of artificial intelligence and statistical analysis. The system
of eye movement data acquisition and their processing used in this work consist of four
separated main blocks (Figure 1). The connections between them tell us that output of one
block serves as input into another block.
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1. INTRODUCTION
Application for Feature Extraction
from Eye Movement Signal Analysis
Figure 1 - A block diagram of the proposed method, the part highlighted in yellow is
concerned with this bachelor thesis
1.1. Main goals
The main objectives of this work are:
1. Develop an application with graphic user interface for automatic mass feature
extraction from results of analysis of eye movement signal. This application should
be able to provide mass feature extraction for multiple analysis files, basic
statistical analysis and visualization of features. For this application is important to
be easily extendible in terms of additional feature extractors.
2. Design the internal structure of feature extractor and document it for facilitation of
further feature extractors creation.
3. Create the mass feature extraction output files structure. These files in Matlab *.mat
file format contain the data used for classification.
4. Validate the application on provided analysis files. Apply the feature extraction
from multiple input analysis files.
5. Contribute in development of Eye Movement Signal Analysis (EMSA) data
structure. This data structure is developed concurrently with the application for
mass feature extraction and serves as analyzed data file format.
1.2. Motivation
Modern technologies of videooculography allow recording the movement of human eye
with the precision needed for detail examination of these movements. Several studies point
the possibility to diagnose serious human conditions from the analysis of eye movement.
Imagine the option of diagnose dyslexia among pre-school children even before they start
to read, diagnose schizophrenia faster than symptoms develop etc. The early treatment or
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1. INTRODUCTION
Application for Feature Extraction
from Eye Movement Signal Analysis
different approach to this people can mean alleviation of disease symptoms and better
quality of life. This possibility can be discovered in studies of eye movements.
Applications of statistical pattern recognition methods are still not common. Classic
statistic methods are mostly used (e.g. hypotheses testing). Statistical pattern recognition
methods can bring us different approach to the eye movements studies. To be able to use
these methods, we need a tool for automatic mass feature extraction from eye movement
signal analysis.
However, there is no application that can be used for feature extraction. Main objective
of this thesis is to create an user application that will support mass feature extraction. As
environment for this application was chosen Matlab, developed by MathWorks. It is
fourth-generation programming language widely used on Department of Cybernetics,
Czech Technical University. The important property of this application is its modulation
character, which means that is possible to add new feature extractors and be able to process
any data files (if the feature extractors are made to process this data type).
1.3. Recording of eye movements
The technology most widely used in the current designs of eye trackers is
videooculography. It is video-based eye tracking technology using a camera with high
sampling frequency. The camera focuses on one or both eyes and records their movement.
The eye tracking system subsequently processes the images into raw data. This data consist
of raw pupil position in coordinates (pixels or angle), pupil size and measurement details
(subject details, stimuli details, etc.).
Prior to this work and recent state, there was a SMI (http://www.smivision.com/) infrared videooculographical device iView 3.0 used to track eye movements of 76 children at
the Department of Neurology, 2nd Medical Faculty, Charles University, Czech Republic
back in year 2003.
Current measurements are executed by using I4Tracking, tracking system provided by
Medicton Group s.r.o. (http://www.medicton.com/). The measuring device consists of high
speed camera attached on glasses (Picture 1), LCD screen and computer, which displays
stimuli and process the data.
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Application for Feature Extraction
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1. INTRODUCTION
Picture 1 - I4Tracking measuring device
1.4. Signal analysis
Data measured by iView system were originally analyzed with Eyemove Toolbox
(Picture 2) developed by Ing. Jakub Snopek in his diploma thesis (2003). The new data
cannot be analyzed by Eyemove Toolbox and redesign of this toolbox for the new data was
declined for various reasons. The source code of this toolbox was used in creating the Eye
Movement Signal Analysis toolbox (EMSA toolbox) for Matlab. EMSA toolbox support
data input from iView system and also I4Tracking system. Support of an additional eye
tracking system is also possible.
Picture 2 - EyeMove Toolbox
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Application for Feature Extraction
from Eye Movement Signal Analysis
1. INTRODUCTION
Task of the signal analysis toolbox is to process the raw data from eye tracker. This data
contain a lot of artifacts, the most significant ones are those made by the eye blink. The
artifacts like this needs to be found and excluded from following analysis. After the
artifacts removal it is possible to analyze the parameters of eye movement, this is primary
the detection of fixations and saccades, also other eye movement components if the VOG
system is fast enough to record this components.
The output from signal analysis is Matlab file *.mat consisting of raw measured data
and analyzed signal data. For each measured subject is exactly one data file.
1.4.1.
Classification of eye movements
Human eye movements consist of several types of movements. The most common types
and their typical values are in Table 1. Recognition of these types is fundamental for
feature extraction.
Type
Saccade
Fixation
Glissade
Smooth pursuit
Microsaccade
Tremor
Drift
Duration [ms] Amplitude Velocity
30 - 80
4 - 20°
30 - 500°/s
200 - 300
10 - 40
10 - 30
200 - 1000
0.5 - 2°
10 - 40′
< 1′
1 - 60′
20 - 140°/s
10 - 30°/s
15 - 50°/s
< 20′/s
6 - 25′/s
Table 1 - This table shows different types of eye movements, their length in milliseconds,
amplitude and velocity (adapted from Holmqvist, 2011).
Saccades are quick, simultaneous movements of both eyes in the same direction from
one fixation to another. They are the fastest movement the body can produce. The fixation
happens when the eye remains still over a period of time (for example when eye stops on a
word when reading - Picture 3). Glissade is a post-saccadic movement of the eye, when the
eye „wobbles‟ a little before coming to a stop. Smooth pursuit is when the eye follows a
moving object. It is driven by different part of brain than saccades. Moving stimuli is
required for smooth pursuit. Microsaccades are very short movements of the eye that are
trying to bring the eye back to the center of fixation (for example after drift). Tremor is a
small movement of frequency around 90Hz, whose exact role is unclear (it can be
imprecise muscle control). Drifts are slow movements taking eye away from the center of
fixation.
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1. INTRODUCTION
Application for Feature Extraction
from Eye Movement Signal Analysis
Picture 3 - Saccades and fixations during reading task (picture adapted from Rayner, 2007)
1.5. Feature extraction
The feature extraction is a way to statistically evaluate the recorded data and compare
the results between the tested subjects. The methods can be divided into four main groups:
position based features, numerosity based features, latency and distance based features and
frequency based features. The result of feature extraction can be numerical value, string,
vector of values or strings. For the mass feature extraction are the results stored in matrixes
for simplification of further classification or data mining.
1.5.1.
Position based features
The most used feature extractors are based on position of eye movement events. The
position duration measures and input/output directions are significant. Some of the position
based feature extractions are prior to numerosity based feature extractions, for example
determining the regressions (quick backward saccades).
The mean durations of eye movement events are mostly used in all researches. The
mean fixation duration is considered as an indication of visual-information-processing
time. This duration can refer to depth of understanding the text.
1.5.2.
Numerosity based features
To count the eye movement events is one of the methods to quantify them. It can be
expressed in absolute numbers (e.g. how many times saccades occurred during certain
task), in proportion to the total number of events or as rate over time. There is often little
point to calculate the total number of saccades or any other event in the whole recorded
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1. INTRODUCTION
Application for Feature Extraction
from Eye Movement Signal Analysis
data. Limiting the counting process on specified tasks is necessary. As exception is for
example the blink rate.
In reading tasks is frequent counting the number of fixations per line or word. Number
of fixations in the area of interest is called fixation density (J.M. Henderson, 1999).
According to review in Jacob and Karn (2003) number of fixations is one of the most used
metrics in usability research. In study of Rubino and Minden (1973) authors found that
children with learning disabilities made significantly more fixations, but there were no
significant differences in fixation’s duration. Also the number of regressions during
reading is one of the most major factors in diagnose of genetic and developmental
disorders (Gilbert, 1953; Pavlidis, 1985; Biscaldi, 1998).
With still images stimuli the number of saccades should be equal to the number of
fixations. For stimuli that elicit smooth pursuit we can count the saccadic rate, it would be
a measure of prevalence of catch-up saccades. Studies reviewed by O’Driscoll and
Callahan (2008) tend to show that participants with schizophrenia have the saccadic rate
much higher than control group subjects. Number of undesirable fixations during smooth
pursuit is also a common feature.
1.5.3.
Latency and distance based features
Latency is a measure of time delay between events, often can be used as reaction time
based features. Most of latency based features are used in dynamic tasks when there are
new objects flashing on the screen and the time to saccadic start is measured. Also eyevoice latency is measured or pupil dilation latency after an event that start the dilation (e.g.
bright light).
Distance based features are not so much often. The eye-mouse distance is used in some
tracking systems measuring the coordination between hand and eye. If tracking system
support tracking of left and right eye simultaneously, the distance between points of gaze
of each eye can be measured.
1.5.4.
Frequency based features
Study of the power spectral density of eye movement signal (Schmeisser, 2001)
indicates that frequency based features has significant meaning during reading tasks. Eye
movements have two components – horizontal and vertical. Frequency analysis can be
used to find some significant properties of both signals (Macaš, 2005).
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1. INTRODUCTION
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from Eye Movement Signal Analysis
1.6. Classification
Classification is based on the output of feature extraction. There are many types of
statistical classification methods. In many cases there are two stages of classification: the
learning stage and the classification stage. In the learning stage are training sets of data
presented to classifier, based on this data classifier can decide during the classification
stage to which set of categories a new observation belongs. Generally, the more of the
training data, the more accurate is the result of classification.
Classification of eye movements usually deals with subgroups of people with some
disorders (dyslexia, schizophrenia, etc.) and healthy test group. As classifiers are mostly
used k-Nearest Neighbor, Bayes classifier or neural networks.
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2. IMPLEMENTATION
Application for Feature Extraction
from Eye Movement Signal Analysis
Chapter 2
2
Imple mentatio n
Implementation
In this chapter is described the eye movement signal input data, their conversion by Eye
Movement Signal Analysis (EMSA) toolbox for Matlab into EMSA files and structures of
EMSA and feature extractors. For mass feature extraction was created the application Eye
Movements Feature Extraction Tool (EMFET), which can be used for mass feature
extraction of any Matlab structure file with adapted feature extractors.
2.1. Signal data
Analyzed signal data by EMSA toolbox were provided in *.mat files readable in
Matlab. These data contains raw measured data, calibration configuration, subject
information, processed signal data etc. Because understanding of EMSA structure is
required for feature extractor creation and no one yet described it, description of EMSA
structure is necessary.
2.1.1.
EMSA structure
The EMSA files are Matlab variables of type STRUCT. This variable type is similar to
Java Object, but has different syntax. I personally contributed on the development of
EMSA structure. Figure 2a and Figure 2b shows the complete structure of EMSA file as is
to date 2013/05/21. Further development of EMSA structure is possible and there can be
major structure changes. For the latest form of EMSA structure please refer to
development coordinator Ing. Martin Macaš.
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2. IMPLEMENTATION
Application for Feature Extraction
from Eye Movement Signal Analysis
Figure 2a - EMSA structure
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2. IMPLEMENTATION
Application for Feature Extraction
from Eye Movement Signal Analysis
Figure 2b - EMSA structure
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2. IMPLEMENTATION
Application for Feature Extraction
from Eye Movement Signal Analysis
2.2. Feature extractors
In fact the feature extractor is Matlab function M-File that has specific structure. The
structure is well described in the file extractor_sample.m stored on attached CD. This
function can have multiple numeric input arguments used for internal calculations. This
values can specify offset, sampling frequency, accuracy etc. It is important to abide the
internal structure of feature extractor for the smooth running of feature extraction.
It is highly recommended to provide the calculation part of feature extractor with trycatch blocks. In case of some calculation failure or missing input data in try block, handle
the error in catch block and provide the right output or NaN.
The feature extractor always counts with only one EMSA file (or any other Matlab data
structure) and it is always the first input argument. If the feature extractor has special input
arguments, they must be specified in arguments cell array. The special input arguments
must have numeric value (use 1 or 0 for Boolean values).
Output of the feature extractor is 1xN cell array. This cell array can contain numbers,
strings, or other Matlab structures. Count N must be always same for one feature extractor,
the same feature extractor cannot give for one data file 1x3 cell array and for another data
file 1x5 cell array.
2.3. Graphical User Interface
Because feature extractor has as input only one analysis file, the Eye Movements
Feature Extraction Tool (EMFET) was made as tool for mass extraction. This application
(Picture 4) was made as Matlab Graphical User Interface (Matlab GUI) and needs Matlab
2009 or newer in order to run properly.
EMFET supports as input data any *.mat Matlab structure, but the feature extractors
must be adapted on this structure.
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2. IMPLEMENTATION
Application for Feature Extraction
from Eye Movement Signal Analysis
Picture 4 - Application window
EMFET support multiple analysis data files extraction by multiple feature extractors.
The application window is separated into 3 panels: in the first panel (Files to analyze) are
analysis files selected, in the second panel (Extractor selection) is specified the folder with
feature extractors and then selected which feature extractors will be used for feature
extraction, the third panel (Arguments) is there to set the individual arguments for each
feature extractor. The selected feature extractors and their arguments settings can be saved
or load.
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2. IMPLEMENTATION
Application for Feature Extraction
from Eye Movement Signal Analysis
Everything about the feature extraction and EMFET application is described in
Application Manual, which is in Appendix.
2.3.1.
Output
The application output is 3 cell arrays: Result, Extractors and Data. Result is MxN cell
array (M is total number of files to analyze, N is sum of selected feature extractors outputs)
containing the feature extraction results. Extractors is 1xN cell array containing the feature
extractors names, input arguments (if feature extractor has any). Data is Mx1 cell array
containing the names of data files.
There are 3 options how to save the computed results and use them in Matlab, for more
information see Application Manual (chapter Saving the result), which is in Appendix.
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3. VALIDATION
Application for Feature Extraction
from Eye Movement Signal Analysis
Chapter 3
3
Validatio n
Validation
To test the application it was necessary to create feature extractors. Because the EMSA
structure is still in development stage and the methods for filtering the signal and feature
detection are not available at this time, the extractors for feature extraction had to be made
for the raw data from the tracking system. These feature extractors can be used for
checking the accuracy of the measurements and calibration of the camera, also can be used
in data mining.
The records of eye movement signals measured by I4Tracking system were used for
feature extraction in this work. They were partially processed by EMSA toolbox and saved
as Matlab *.mat files. Each file corresponds to one measured subject, whose eye
movements have been recorded and analyzed. All these fifteen subjects were without eye
disorders and data serves as test data for EMSA toolbox and feature extraction creation.
3.1. Feature extractors description
3.1.1.
Out of screen proportion (out_of_screen,
out_of_screen2)
The recorded data (raw_position_x, raw_position_y) are taken from the tracking
system. How accurate the data are depends on the conditions of measurement and tracking
system abilities. Mostly the head of the subject is not firmly attached (to be not disturbed
and feel more naturally). When the subject moves the head and there is no compensation
from the side of the tracking system, then the data move off the screen into negative values
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3. VALIDATION
Application for Feature Extraction
from Eye Movement Signal Analysis
or values higher then screen resolution. The perfect example is on Figure 3, the tracking
system in this case I4Tracking does not compensate the movement of the head and part of
data is out of screen.
Figure 3 - 33.4% of signal data are out of screen
This can cause issues in further analysis of data or feature extraction. Also the stimuli
picture when given under the data as background does not correspond with the data, which
can be very confusing.
If the tracking system automatically compensate the head movement, or the
compensation is done by EMSA toolbox analysis, there can still be some out of screen
data. For example when the subject just look outside the screen (e.g. on measurement
supervisor or some distraction).
The feature extractors out_of_screen and out_of_screen2 gives the percentage of data
outside of screen in range 0-100%. If there is no compensation of the head movement, the
higher this number is the more movement of head this subject made. But if there is the
compensation of the head movement, the higher this number is the more distracted was the
subject during the measurement and this measurement can be considered as faulty.
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Application for Feature Extraction
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3. VALIDATION
The out_of_screen feature extractor considers all tasks in file. Instead out_of_screen2
consider only one task in file, the task number is given as argument and is 1 in default.
3.1.2.
Stimuli type (stimuli_type)
In comparison of feature extraction from two and more data files is often essential that
the extracted features are from the same stimuli. This feature extractor lists the stimuli type
of task number given as argument (default 1).
3.1.3.
Task time (task_time)
In most cases the stimuli have not specified projection duration and the subjects tell the
supervisor when they are done with the task. The time they needed for task is feature, that
can help in diagnose and assessment if the measurement is successful. The example how
task time can differ by subjects is plotted in Figure 5. All these subjects had to make the
same task called dots2 (Figure 4). The stimulus for task dots2:”Look through the dots one
by one and knock by hand when you will be over.” The results are in milliseconds.
Figure 4 - dots2
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Application for Feature Extraction
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3. VALIDATION
Figure 5 - Task time of different subjects
3.2. Mass feature extraction
In this section is the mass feature extraction tested. For the capability of mass feature
extraction the application Eye Movements Feature Extraction Tool (EMFET) was created.
As the input were used the 15 data files in EMSA structure measured by I4Tracking
system. The output of the test feature extraction is shown below in Tables 2-4.
Table 2 saved as variable extractors is where the feature extractors names and
arguments are stored. The structure of the cell content is: ‘feature extractor
name’_‘argument values’/‘index’ . Feature extractor name is always used, argument values
are used only if feature extractor support variable arguments, index is used only if one
feature extractor returns more than one result (in that case each result is in one cell).
out_of_screen
'out_of
_screen2_6'
'stimuli
_type_6'
'task_ti
me_6'
'task_ti
me_2'
out_of_screen2_6
stimuli_type_6
task_time_6
task_time_2
Table 2 - extractors
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Application for Feature Extraction
from Eye Movement Signal Analysis
3. VALIDATION
result20121213_152458.mat
result20121213_153917.mat
result20121213_154811.mat
result20121213_155653.mat
result20121213_161159.mat
result20121213_161924.mat
result20121213_163340.mat
result20121213_164358.mat
result20121213_165218.mat
result20121213_170206.mat
result20121213_171534.mat
result20121213_173252.mat
result20121213_174750.mat
result20121213_175426.mat
result20121213_175844.mat
Table 3 - file_names
0.19
7.03
0.01
1.48
0.20
0.02
0
0
3.71
0
0
0
0
0.02
0.70
0
33.37
0
0
0
0
0
0
15.95
0
0
0
0
0
0
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
Kompsm2
21316
16289
9735
8661
8661
5820
10837
9178
9179
7429
8203
6641
6936
6385
6654
11266
14663
10416
6606
7387
3791
7487
6038
8703
5390
12281
5955
5289
6472
6171
Table 4 - results
Table 3 saved as variable file_names is where the input data filenames are stored. Table
4 is the results table, into this table is stored the results of extraction. If Table 2 has N cells
and Table 3 has M cells, the size of Table 4 is MxN, in other words the size of the results
table is number of extractors’ results times number of input files.
19/28
4. CONCLUSION
Application for Feature Extraction
from Eye Movement Signal Analysis
Chapter 4
4
Conclusio n
Conclusion
Application for feature extraction from eye movement signal analysis was proposed in
this work. This application manages mass feature extraction from one or more input data
files in Matlab format. The format of input data is independent on Eye Movements Feature
Extraction Tool (EMFET) application. Output files from this application are in Matlab file
format, that can be used for classification, diagnose or in data mining. User manual for this
application is attached in Appendix.
The important part of this thesis is design of the feature extractor structure. Feature
extractors are Matlab single-function M-Files automatically recognized by EMFET
application with designated structure (structure is described in Chapter 2.2. and in file
extractor_sample.mat attached on CD). They have one mandatory argument, which is the
single input analyzed data. From this is evident the 1:N relation between the input data
structure and the feature extractor. The feature extractors can have extra variable
arguments that are set before each feature extraction in the graphical user interface.
EMFET is capable of saving and loading the settings of selected feature extractors and
their variable arguments.
For testing purposes were created 4 feature extractors (they are described in Chapter
3.1.) for EMSA files. The complete structure of EMSA file is described in Chapter 2.1.1.
for further feature extractor creation. As input data served 15 measurements of healthy
subjects measured via I4Tracking system. They were partially processed by Eye
Movement Signal Analysis toolbox. EMFET application were used for the mass feature
extraction from these measurements, thereby was verified the functionality in practice.
20/28
4. CONCLUSION
Application for Feature Extraction
from Eye Movement Signal Analysis
4.1. Future work
There is a lot of space for the future work. At first creating more feature extractors is
necessary for a successful classification. The feature extractors based on features described
in Chapter 1.5. would be appropriate to create for EMSA files.
The EMFET application can be redesigned as server-client application or web
application. This would cause end of problems with Matlab licensing, Matlab would be
only on server machine with single Matlab license. All the clients will use the numerous
possibilities of server machine.
Improving the EMSA toolbox internal methods (this is related to EMSA structure) is
also possible. The current status is not sufficient for studying of eye movements and there
need to be a lot of improvements.
Figure 1 shows the system of eye movement data acquisition and their processing, the
blocks are separated as well as the software for analysis of eye movement. In one day this
could be all connected in one big application, which will do everything.
21/28
Table of Contents
INTRODUCTION .................................................................................................. 24
STARTING THE APPLICATION .......................................................................... 24
Set Matlab search path .................................................................................................................. 24
Start the application ....................................................................................................................... 25
EXTRACTION CONFIGURATION ....................................................................... 26
Select the extraction data .............................................................................................................. 26
Load and select feature extractors ............................................................................................... 26
Set parameters of feature extractors ........................................................................................... 27
Save/Load the configuration ......................................................................................................... 27
EXTRACTION ...................................................................................................... 27
Saving the result ............................................................................................................................ 28
Introduction
This application the Eye Movements Feature Extraction Tool (EMFET) was created to
simplify the extraction of eye movements symptoms.
To run this application you need Matlab version 2009 or newer.
Starting the application
Set Matlab search path
There are two ways to add the application folder to a Matlab search path, use one of these:
1. Set your current Matlab folder to folder with EMFET. To check your current
Matlab folder type into Matlab command window:
>> pwd
ans =
C:\EMFET
2. Add EMFET folder to Matlab search path. You can do it temporarily by typing into
Matlab command window:
>> path (path,’*folder*’)
Note: change *folder* to EMFET folder, for example
C:/EMFET
or permanently using the Matlab Set Path dialog box (use the Add Folder button) as
you see on Picture 1.
24
Picture 1 - Matlab Set Path dialog box
Start the application
Start the EMFET application from the Matlab command window, the syntax is:
>>
>>
>>
>>
emfet
result = emfet
[result extractors] = emfet
[result extractors data] = emfet
[result extractors data] = emfet saves the last computed results of application into
Matlab workspace when you quit application. There are several other ways how to import
the result into Matlab workspace, see chapter Saving the result.
The application will start in new window as you see on Picture 2.
25
Picture 2 - Application window
Extraction configuration
Select the extraction data
Press the Search button in panel Files to analyze and locate EMSA files (or any other
Matlab structure *.mat files) in your computer. You can choose multiple files in one folder
(use the mouse selection or CTRL+click to select more than one file).
Load and select feature extractors
The default folder for feature extractors is extractors subfolder in EMFET folder. If you
want to use other feature extractors then copy the feature extractor M-files to this folder
and restart the application, or use the Search button in panel Extractor selection and locate
the folder with your feature extractors M-files in your computer. Feature extractors then
appear in Available extractors’ listbox. Files in the chosen folder that are not extractors are
displayed on Matlab Command Window.
Using the arrow buttons select feature extractors you want to use on selected data files. The
double arrow button adds all feature extractors from one listbox to another. If you want to
26
use one extractor twice (or more), for example with another parameter setting, simply add
more same extractors in the Selected extractors listbox.
Set parameters of feature extractors
If the feature extractor supports variable parameters values, you can set them in panel
Arguments. In the listbox Selected extractors highlight the feature extractor you want to
modify, uncheck Default Values checkbox and modify the parameters. This can be done
for all selected feature extractors.
Save/Load the configuration
Application allows saving the selection of extractors and their parameter settings. Once
you have selected the feature extractors and modified the parameters press the Save button,
the Save dialog appears (Picture 3), enter the settings name (for example “My settings
18.4.2013”) and confirm the save with OK button. The saves will remain even if you close
the program and Matlab.
Picture 3 - Save dialog
Before loading the configuration settings make sure that you have feature extractors you
want to load in Available extractors listbox (if not, see Load and select feature extractors).
Press the Load button, the Load dialog appears (Picture 4), choose the one you want to
load and press Load button.
Picture 4 - Load dialog
Extraction
Once you have selected the files to analyze and extractors you want to use press the Extract
button. Matlab automatically calculate the result cell arrays and save dialog will appear.
27
This is one of three options how to save computed results. If you cancel this save dialog,
you can still save the result using the other two methods.
Saving the result
As mentioned before there are 3 options how to save computed results and use them in
Matlab:
1. Save variables using save dialog, that appears with Extraction. Variables are stored
in *.mat file, which can be easily load into Matlab workspace, see Matlab load
function.
2. Start the application using syntax mentioned in chapter Start the application. Then
when you quit the application, Matlab will store the last computed results into
variables you defined.
3. After every extraction there is automatically saved the results into file
last_result.mat in the folder with EMFET.
28
BIBLIOGRAPHY
Application for Feature Extraction
from Eye Movement Signal Analysis
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