Recent results on structural pattern recognition for Fusion massive databases
ABSTRACT Physics studies in fusion devices require statistical analyses of a large number of discharges. Given the complexity of the plasma and the non-linear interactions between the relevant parameters, connecting a physical phenomenon with the signal patterns that it generates can be quite demanding Up to now, data retrieval has been typically accomplished by means of signal name and shot number. The search of the temporal segment to analyze has been carried out in a manual way. Manual searches in databases must be replaced by intelligent techniques to look for data in an automated way. Structural pattern recognition techniques have proven to be very efficient methods to index and retrieve data in JET and TJ-II databases. Waveforms and images can be accessed through several structural pattern recognition applications.
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ABSTRACT: Fusion measurement systems generate similar waveforms for reproducible behavior. A major difficulty related to data analysis is the identification, in a rapid and automated way, of a set of discharges with comparable behaviour, i.e. discharges with "similar" waveforms. Here we introduce a new technique for rapid searching and retrieval of "similar" signals. The approach consists of building a classification system that avoids traversing the whole database looking for similarities. The classification system diminishes the problem dimensionality (by means of waveform feature extraction) and reduces the searching space to just the most probable "similar" waveforms (clustering techniques). In the searching procedure, the input waveform is classified in any of the existing clusters. Then, a similarity measure is computed between the input signal and all cluster elements in order to identify the most similar waveforms. The inner product of normalized vectors is used as the similarity measure as it allows the searching process to be independent of signal gain and polarity. This development has been applied recently to TJ-II stellarator databases and has been integrated into its remote participation system. (c) 2007 Elsevier B.V. All rights reservedFUSION ENGINEERING AND DESIGN. 01/2008; 83(1):132-139.
Recent results on structural pattern recognition for
Fusion massive databases
J. Vega1, G. Rattá1, A. Murari2, P. Castro1, S. Dormido-Canto3, R. Dormido3, G. Farias3, A. Pereira1, A. Portas1, E. de
la Luna1, I. Pastor1, J. Sánchez3, N. Duro3, R. Castro1, M. Santos4, H. Vargas3
1Asociación EURATOM/CIEMAT para Fusión. Avda. Complutense, 22. 28040 Madrid, Spain
2Consorzio RFX-Associazione EURATOM ENEA per la Fusione. I-35127 Padua, Italy
3Dpto. de Informática y Automática. Universidad Nacional de Educación a Distancia. Madrid, Spain
4Dpto. de Arquitectura de Computadores y Automática. Universidad Complutense. Madrid, Spain
Abstract – Physics studies in fusion devices require statistical
analyses of a large number of discharges. Given the complexity
of the plasma and the non-linear interactions between the
relevant parameters, connecting a physical phenomenon with
the signal patterns that it generates can be quite demanding. Up
to now, data retrieval has been typically accomplished by means
of signal name and shot number. The search of the temporal
segment to analyze has been carried out in a manual way.
Manual searches in databases must be replaced by intelligent
techniques to look for data in an automated way. Structural
pattern recognition techniques have proven to be very efficient
methods to index and retrieve data in JET and TJ-II databases.
Waveforms and images can be accessed through several
structural pattern recognition applications.
Keywords – Data mining, information retrieval, image
processing, structural pattern recognition.
Some plasma behaviors, as a result of unexpected events
and instabilities, only become apparent in an intermittent way.
This fact can complicate the interpretation of their physical
nature and their potential effects on the plasma confinement.
The starting point to analyze these phenomena is to find a
number of occurrences high enough to formulate hypotheses
with a sufficient statistical basis. The search of events is
carried out in a manual way by means of visual data analysis.
Visual inspection of signals allows the recognition of certain
patterns that can be used to identify the presence of non-
standard behaviors. The aim of this searching process is to
determine both the shot number and the time interval where
the patterns appear.
Nowadays, data retrieval methods can no longer be based
on manual searches according to signal name and shot
number. First, the pulse length of the experiments is
increasing significantly. The longer the pulse, the more
tedious is the manual pattern search. Second, the rapid
increasing of imaging diagnostics should be considered. For
example, fast cameras may acquire images with a rate of
hundreds of frames per second and, therefore, the manual
selection of a representative image for a particular event
becomes a cumbersome procedure. Third, it should be noted
that very large databases, with millions of signals (for
example, TJ-II is a medium size device that acquires 500
signals/discharge and has stored about 18000 discharges) and
Tbytes of data, have to be analyzed. For instance, JET may
produce over 10 Gbytes of data per shot, although the typical
rate is 5 Gbytes/discharge.
New models for data retrieval have to take advantage of
the fact that fusion diagnostics produce similar signals for
reproducible behaviors. This means that diagnostics translate
physical properties into patterns with a correspondence
between the plasma physical properties and the structural
shapes that are generated in the signals. Therefore, this direct
link allows the introduction of a new paradigm for data
access. Instead of using the shot number as input parameter
and the signal samples as output data, a more practical
criterion would be to ask for a pattern and to receive the pulse
numbers and the locations (time instant and/or spatial
position) where the pattern appears.
A first approach for pattern oriented data retrieval is the
use of the structural forms of the signals. The presence of
characteristic patterns in waveforms (bumps, unexpected
amplitude changes or abrupt peaks) and images (high
intensity zones or specific edge contours) convert structural
pattern recognition techniques in optimal methods to attain an
automated and efficient data access. Two very generic
approaches, based on structural pattern recognition
techniques, have been developed for general purpose data
retrieval in fusion. First, the entire signal (ES) approach
allows searching for similar images or waveforms  from a
1-4244-0830-X/07/$20.00 ©2007 IEEE.
given one. An entire signal is a complete image or waveform.
Complete waveforms are defined for the same temporal
interval from a particular event. Examples are: a 40 s interval
from the plasma start, a 10 s segment from the beginning of
the neutral beam injection or 5 s after an L-H transition.
Secondly, another structural approach has been developed :
patterns in signals (PIS). PIS allows seeking for specific
patterns within signals.
This article summarizes both techniques and shows
specific applications to time-series data and images in
databases of two different fusion devices: the TJ-II stellarator
and the JET tokamak. TJ-II is a medium sized stellarator
(heliac type)  located at CIEMAT, Madrid (Spain). JET 
is the biggest fusion device in the world and it is located in
Section II of the article introduces the notion of signal
collections to put together comparable data. Section III
summarizes the main concepts to consider in a general pattern
recognition problem. Section IV is devoted to describing the
application of structural pattern recognition techniques to
Fusion databases. Sections V and VI review respectively the
ES and PIS approaches. Section VII is a discussion.
II. SIGNAL COLLECTIONS
A signal is any kind of data that describes a particular
measurement during a discharge and contains some
information. Depending on the specific representation of the
data, signals can be of several types. Firstly, we have bi-
dimensional data. The samples are defined by ordered pairs
(x, y). Temporal evolution signals are a particular case of bi-
dimensional data where one of the coordinates is time (fig.
1a). Secondly, contour maps are often encountered. They are
3-dimensional representations with two spatial coordinates
and the corresponding amplitude (fig. 1b). Thirdly, images
are becoming every day more frequent. Each pixel is
described by two spatial coordinates, a color intensity and a
forth dimension to distinguish the red, green and blue color
components (fig. 1c). Finally, it should be mentioned that as
personal computers are providing more capabilities on
computing and storage, video movies are becoming very
popular diagnostic signals, and very promising results are
being obtained with infrared and visible cameras in JET .
Signals are grouped into collections for pattern oriented
data retrieval. A signal collection is the complete set of
recorded signals for all the discharges of interest. As a first
example, the plasma current collection is made up of all
temporal evolution signals that provide the plasma current in
a Tokamak. A second example of collection could be the set
of movies of an infrared video camera. Generally speaking,
any data representation to describe a particular measurement
(usually on a shot to shot basis) is a collection. The existence
of collections obeys to the need of grouping comparable data
to make pattern searches easier through equivalent data
MAIN CONCEPTS IN PATTERN RECOGNITION
Due to the fact that the new model for data retrieval should
be pattern oriented, a straightforward approach would be the
use of pattern recognition techniques  for data access.
Pattern recognition is the scientific discipline dealing with
methods for object description and classification. Therefore,
two main concepts arise: object description and classification
systems. A fundamental third concept in pattern recognition,
independent of whatever approach we may follow, is the
notion of similarity. Two objects are recognized as similar
because they have valued common attributes.
It should be noted that a high dimensionality is an issue in
pattern recognition techniques because the computational
effort increases with the dimensionality of the problem. In
Fusion massive databases, the dimensionality depends not
only on the number of signals (millions of waveforms, images
and video movies) but also on their size (millions of samples
per waveform and hundreds of millions of pixels per movie).
A. Object description
Object description is the process by means of which a
proper representation of the objects is achieved for
classification purposes. The process consists of extracting
features or attributes that are of distinctive nature. After
feature extraction, objects are always represented by the
corresponding feature vectors. The process has a double
functionality. On the one hand, it translates characteristics of
the objects into attributes that can be managed by a computer
system. On the other hand, feature extraction is used to reduce
the dimensionality of the problem as much as possible.
Fig. 1. Examples of time-series data (a), contours (b), and images (c)
B. Classification system
Classification systems are used to index the objects
according to some criteria. This means the creation of
different clusters (classes) to show the grouping in the data.
Creating classifiers is a learning problem. Learning refers to
some form of algorithm to assign each object to a cluster.
There are two common types of learning problems, known as
supervised learning and unsupervised learning. Supervised
learning is used to estimate an unknown (input, output)
mapping from known (input, output) samples. The term
‘supervised’ denotes the fact that output values for training
samples are known. In the unsupervised learning scheme,
only input samples are given to a learning system, and there is
no notion of the output during the learning [7, 8].
C. Similarity measure
This concept is necessary to compare how similar two
objects are. It requires the introduction of a distance between
the features or attributes of the objects (in the mathematical
sense) to be used as a proximity measure.
STRUCTURAL PATTERN RECOGNITION
Recorded signals from diagnostics are used to analyze the
plasma physical properties. Such properties can be identified
by the presence of associated patterns (structural shapes) in
the data. The recognition of structural shapes plays a central
role to distinguish particular behaviors. Making use of this
fact, computational methods can be developed to update the
classical model of data retrieval with a new one based on
searching for data according to physical criteria. The
traditional method, based on asking for shot number and
returning the signal samples, does not provide pattern
locations. Patterns inside the signals have to be found by
means of data inspection. A more powerful paradigm for data
retrieval is founded on asking for patterns inside signal
collections and obtaining the discharge numbers and the
pattern location within the signals.
Taking into account the high dimensionality of Fusion
databases, the main challenge to put into operation the new
paradigm can be summarized with a single word: efficiency.
In this context, efficiency means not to traverse the entire
database when a specific pattern is searched, but to develop
intelligent mechanisms to reduce the searching space just to
the most probable signals of containing a similar pattern.
The crucial element to achieve efficiency in this structural
pattern recognition problem is the classification system. In a
linear approximation, looking for similar structural forms
inside a signal collection means to compute the similarity
measure between all pairs of feature vectors. However, the
classification system allows the indexation of the feature
vectors in such a way that clusters group similar objects.
Therefore, each cluster represents a reduced searching space
in which the more likely objects to be similar can be found.
To look for structural patterns inside a signal collection,
some previous steps are required. Firstly, features to describe
the signals must be chosen. Secondly, clustering criteria to
group the data into convenient clusters have to be defined.
Thirdly, a similarity measure is needed to be able to compare
how similar (or dissimilar) two feature vectors are.
After the creation of the indexation system, the search of
patterns can be carried out. Given a target pattern, the
searching process of similar patterns is accomplished in three
steps: feature extraction, feature vector classification and
similarity factor computation. The former is essential to
classify the target pattern into one of the existing clusters and,
hence, the target pattern is grouped together with the more
similar ones. The similarity measure is only computed
between the target feature vector and the feature vectors of
the cluster and, therefore, the search method avoids traversing
the whole database.
As it was mentioned above, two different approaches were
developed for data retrieval with structural pattern recognition
techniques: the ES and the PIS methods. Table I summarizes
applications of both techniques to several signal collections
(waveforms and Thomson Scattering (TS) images) of
different databases (JET and TJ-II).
V. ENTIRE SIGNAL APPROACH
The applications of the ES technique to JET and TJ-II
waveforms use the Haar wavelet transform  as feature
extractor. This selection allows a strong reduction of the
dimensionality and it retains the waveform time and
The indexation system is based on a multi-layer
classification system whose clustering criteria may evolve in
a flexible and dynamical way. Individual clusters can be split
at any moment to reach an optimal classification. At present,
two layers have been considered. The first one divides the
collection into clusters that group shots with the same pulse
length. Each first layer cluster can be split into several ones
according to a structural shape criterion (fig. 2). The figure
shows how the cluster refinement produces groups with lesser
number of signals. In this case, the grouping was carried out
according to similarity values.
SUMMARY OF STRUCTURAL PATTERN RECOGNITION APPLICATIONS
Collection Method Feature
PIS Slopes Fitted
The similarity factor is the normalized inner product (NIP).
Actually, the absolute value of this quantity has been chosen
to measure the similarity of two feature vectors uw and vw.
This definition was taken by several reasons. First, the
straightforward: two unitary vectors are equal if the inner
product is 1. If the value is 0, both vectors are orthogonal and
no similarity exists. Second, this NIP is independent of
amplification factors. Signals differing exclusively in a gain
factor are recognized as equal waveforms (similarity 1).
Third, the NIP is also independent of signal polarities.
Figure 3 shows the application of the ES technique to a
bolometry signal collection of the TJ-II database. The
waveforms are raw data not calibrated in an absolute way. It
should be emphasized that signals differing in gain and
polarity are recognized as similar signals.
Java applications for data retrieval are accessible for
concurrent execution from the TJ-II remote participation
system (for TJ-II databases) and the JET data access
environment (for JET databases).
of the dot product is
Computation times to complete a searching process were
measured in two different computer environments with a
single layer classification system based on discharge length.
A first environment with 128 clusters was created with the
Matlab software package on a Windows XP Pentium IV
computer. The searching time is the sum of three different
times: feature extraction of the target waveform, feature
vector classification into one of the clusters of the
classification system and NIP computation of the target
feature vector with all feature vectors in the previous cluster.
The first two times are negligible in comparison with the third
one. A mean value can be established as 18 ms per signal
present in the second step cluster. A second environment with
256 clusters of waveforms was tested at the JAC Linux
Cluster at JET (a high performance cluster of 181 Athlon
processor cores). The searching time was 1 ms/waveform in
Concerning the additional storage requirement for the
classification system, the worst case needed an extra 17% of
the space filled by the signal collection.
The ES approach has been also applied to images. In
particular, the collection is made up of the images from the
TJ-II Thomson Scattering CCD camera. One image is
collected per discharge and five different kinds of images are
possible, depending of the type of measurement: CCD camera
background, stray light, electron cyclotron heating (ECH)
phase, neutral beam injection (NBI) phase and cut off density
Feature extraction is accomplished by means of a Haar
two-dimensional wavelet transform . The classification
system is based on a supervised clustering method with five
classes (one per possible measurement). The similarity
measure is computed with the Euclidean distance between
feature vectors. In this particular case, the Euclidean distance
provides a better discrimination than the NIP because it is not
necessary to reach the 6th or 7th decimal in the similarity
factor to distinguish images.
1st layer cluster
27 waveforms27 waveforms
2nd layer cluster
11 waveforms11 waveforms
2nd layer cluster
11 waveforms11 waveforms
2nd layer cluster
2 waveforms2 waveforms
2nd layer cluster
3 waveforms3 waveforms
1st layer cluster
2nd layer cluster
2nd layer cluster
2nd layer cluster
2nd layer cluster
Fig. 2. Example of a cluster splitting with electron cyclotron
emission (ECE) waveforms from the JET database
Fig. 3. ES technique applied to a TJ-II database collection. Waveforms
whose difference is gain factor or polarity are recognised as similar
To search similar signals to a target one, the procedure
performs feature extraction and the classification into one of
the five clusters. It is attained by means of a linear
discriminant function based on Support Vector Machines
(SVM) in a one-versus-the-rest approximation. Similarities
are computed with the feature vectors of the cluster.
PATTERNS IN SIGNALS APPROACH
This approach allows the search of patterns within time-
series data. This is a big challenge in data retrieval taking into
account the very large volume of Fusion databases.
Patterns can be considered as composed of simpler sub-
patterns. The most elementary ones are known as primitives.
Primitives are represented by characters, converting the
pattern recognition problem into a pattern-matching problem.
The description of objects in this kind of pattern
recognition systems is difficult to implement because there is
no general solution for extracting structural features
(primitives) from data. Primitive extractors can be developed
to extract either the simplest and most generic primitives or
the domain specific primitives that best support the
subsequent searching task. The former are domain
independent and the knowledge content is reduced to a
minimum. The latter requires strong domain knowledge and
this can be an issue for the wide application of the technique.
Therefore, to solve general purpose needs, it is better to use
domain independent feature extractors.
Bearing in mind that the feature extraction tries to reduce
the problem dimensionality, any signal can be divided into
segments of equal temporal length and each segment is fitted
with a straight line through a least squares minimization
process (fig. 5). Then, segments are encoded according to a
discrete set of values (code alphabet). The definition of code
alphabets enables the description of time-series data as
strings, instead of representing the signals in terms of
multidimensional data vectors. The labels of the segments are
based on the slope of the straight lines (fig. 5). For this
reason, this method is called “the slope method”.
Due to the fact that waveforms are represented by strings,
searching for patterns means looking for characters.
Therefore, database technologies must help in the
development of the classification system. One particular
database model offers a unique combination of power,
flexibility and universal acceptance: the relational model .
In addition, the relational model provides enough flexibility
to retrieve combinations of data. For example, instead of
searching for an exact match of slopes, it is easy to include in
the query the search of adjacent slopes or even, the search of
just the inverse polarity sequence (fig. 5). It should be
mentioned that a relational database cannot be seen as a
clustering system in the most pure sense, but it is a very
efficient indexing system to retrieve data.
The application of this technique to the TJ-II database was
developed with the Microsoft-Access relational database. It is
discussed in  and a variant of this method was developed
for JET databases. Looking for reducing the number of
primitives to represent a signal, segments of variable temporal
length were considered (fig 6). This length is defined by the
number of samples to fit the signal with a straight line (least
squares minimization), but maintaining the fit error lesser
than a certain factor, F, depending on the waveform standard
Each new segment starts with the fit of three points to a
straight line and samples are added (one by one) while the fit
error is smaller than F. The temporal length (∆t) and the
amplitude difference (∆A) between the ends of each segment
(fig. 6) are stored to compute the similarity in pattern
Fig. 4. CCD camera images corresponding to spray light (a), ECH
phase (b), NBI phase (c) and cut off density (d).
Fig. 5. The slope method. Signals are fitted with straight lines and
the labels are the slopes of the straight lines
input pattern primitive sequence
matching pattern 1 in the database
matching pattern 2 in the database
matching pattern 2 in the database
direct polarity sequencedirect polarity sequence
ac e dz
d e ca
inverse polarity sequenceinverse polarity sequence
input pattern primitive sequence
matching pattern 1 in the database
ac e dz
d e ca
When selecting a pattern in a signal, (for instance a pattern
made up of m characters ‘C1C2…Cm’), the searching process
queries to the relational database for this string and it returns
all records containing ‘C1C2…Cm’. At this point, it is
necessary to sort the results by means of a similarity measure
between the target pattern and the returned data.
The similarity factor is defined through the mean value of
NIPs over all the segments that form a pattern, where the
NIPs are computed with the ordered pairs (∆t, ∆A) of each
segment of the signals to compare.
, #segments in the pattern
u i v i
With this definition the similarity is a real number between
0 (no similarity at all) and 1 (equal signals).
The slope method with variable temporal length segments
is accessible in a concurrent way for multiple users from the
JAC Linux Cluster of JET. It uses the PostgreSQL relational
database (http://www.postgresql.org). A searching example is
shown in figure 7. At the top, the target pattern appears. It is
found with similarity 1 and similar patterns can be seen inside
the other waveforms.
Computation time for data searching depends on the
pattern to search and also on the flexibility level required in
the query. Typical times are seconds. Additional storage
requirement for the classification system is, in general, a
small fraction of the space needed for the signal collection.
( ) ( )
target patternretrieved data
( )(,)and ( )(,)
Structural pattern recognition techniques are an efficient
way to implement a pattern oriented data retrieval paradigm.
The smoothing level to extract signal characteristics in the
feature extraction process is related (in a direct way) to the
degree of dimensionality reduction accomplished in the
process. Therefore, fast events (like ELMS or MHD modes)
require low smoothing levels. The cost for this is not to
achieve high dimensionality reductions. As a consequence,
higher additional storage for the classification system will be
There is not a single criterion to develop classification
systems. However, care should be taken to avoid the creation
of clusters with only one or two shots.
The authors wish to thank Prof. Sebastián Dormido
Bencomo (UNED) and Prof. Jesús Manuel de la Cruz (UCM)
for their constructive comments and help.
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Fig. 6. The slope method with segments of variable temporal length
Shot: 69146Shot: 69146
Shot: 69145Shot: 69145
Shot: 68593Shot: 68593
Shot: 68453 Shot: 68453
Shot: 68454Shot: 68454
Similarity: 1.0000 Similarity: 1.0000
Similarity: 0.9998Similarity: 0.9998
Similarity: 0.9986 Similarity: 0.9986
Similarity: 0.9956Similarity: 0.9956
Similarity: 0.9952 Similarity: 0.9952
Fig. 7. Search of similar patterns in JET. The waveforms correspond
to ECE signals to measure electron temperature. Variable temporal
length primitives were used. Note that the all patterns found follow
the same behaviour but during different time: 1) a fall; 2) a fast slope
(more abrupt in shot 68593 but codified with the same code); 3) a flat
zone; 4) a fast rise; 5) a new flat top