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Solar filaments detection using parallel programming in hybrid architectures

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 Solar Filaments Detection Using Parallel Programming in
Hybrid Architectures
Fabio Andrijauskas
School of Technology - University of Campinas
Rua Paschoal Marmo, 1888 - Limeira -
13484-332
32,038 São Paulo, Brazil
fabio.andrijauskas@gmail.com
ABSTRACT
There are several projects and missions designed to strictly
observe the Sun. These projects usually produce a large
amount of information embedded in images. The analysis
of such information is valuable for the study and monitoring
of solar storms that can affect telecommunications, for ins-
tance. The databases sizes with sun image are huge. Several
projects are producing images of the Sun and exists a con-
siderable amount of stored images. Combining image pro-
cessing algorithms with parallel programming techniques we
can compute such information faster and a major volume.
This paper describes our parallel OpenMP-MPI hybrid solu-
tions for processing Sun images, and our results obtained in
a hybrid system, i.e. a cluster with several multi-core nodes.
Specifically, we present two methods to detect and catego-
rize solar filaments in hybrid systems: Filament Diffusion-
Detection based on graphs and Morph Detection, based on
morphological operators. The results show that the Fila-
ment Diffusion-Detection based on graphs detects approxi-
mately 80% of the filaments, with a 326-fold speed-up over.
In turn, Morph Detection detects 58% of the objects with
a 54-fold increase in speed. Overall, these results show that
our OpenMP-MPI combination works well for hybrid ar-
chitectures, but more optimizations are needed to improve
accuracy.
Keywords
solar filaments, parallel programming, hybrid systems
Categories and Subject Descriptors
J.2 [Physical Sciences and Engineering]: Astronomy;
I.4.3 [Image Processing and Computer Vision]: En-
hancement—Filtering; I.4.6 [Image Processing and Com-
puter Vision]: Segmentation—Edge and feature detection;
D.1.3 [Programming Techniques]: Concurrent Progra-
mming—Parallel programming
Permission to make digital or hard copies of all or part of this work for
personal or classroom use is granted without fee provided that copies are
not made or distributed for profit or commercial advantage and that copies
bear this notice and the full citation on the first page. To copy otherwise, to
republish, to post on servers or to redistribute to lists, requires prior specific
permission and/or a fee.
AstroHPC’12, June 19, 2012, Delft, The Netherlands.
Copyright 2012 ACM 978-1-4503-1338-4/12/06 ...$10.00.
41
André Leon Sampaio Gradvohl
School of Technology - University of Campinas
Rua Paschoal Marmo, 1888 - Limeira -
13484-332
São Paulo, Brazil
gradvohl@ft.unicamp.br
1. INTRODUCTION
The Sun produces its energy by fusing hydrogen atoms
into helium. In this process, there are several events that
may occur. For example, solar storms can be of high in-
terest because they can lead to problems in telecommunica-
tions like GPS signal interruptions, satellite routes changes
or destruction. In addition, those events may cause electric-
ity transmission problems such as the overload of electric
transmission lines, caused by the geomagnetically induced
current caused by the solar storm. These catastrophic sce-
narios could be avoided if the solar storm is detected with
enough time to turn off satellites or to reduce the energy in
the transmissions lines.
The solar storms are characterized by several features.
One of those features is the arising of filaments on the surface
of the Sun. Those filaments are visible in the Hα images.
They are some plasma from the sun sustained by the mag-
netic fields and with high density. They are cooler than the
sun surface. That is why they are presented in a darker
color. Figure 1 shows an example of solar storm events, fea-
tured a filament. Notice that the darker ribbons of the Sun
are the filaments.
Figure 1: Sun image obtained by the Big Bear Solar
Observatory. A filament was manually detached.
The detection of such events is very important for space
weather monitoring because several solar filaments are asso-
ciated with the sun coronal mass ejection (CME) [5].
The images of the Sun are produced in large quantity and
with high resolution. For example, The Big Bear Solar Ob-
servatory produces approximately 600 images of the Sun at
2048 × 2048 resolution per day. The NASA Solar Dynamics
Observatory also produces about 1.5 terabytes per day of
Sun images. Considering the missions that study the uni-
verse all together, the amount of research data available by
2020 will reach 60 petabytes [1]. To process this amount of
information in a reasonable time, it is necessary to use a lot
of computing power. Parallel processing techniques will, for
sure, be very useful in achieving this goal [9] [10].
1.1 Related work
Solar filaments detection methods were already addressed
in other works. In [8], an automatic solar filament detection
algorithm is presented. The algorithm is based on image en-
hancement, pattern recognition and mathematical morphol-
ogy methods. Also, [11] focuses on the techniques which uses
mathematical morphology to detect solar filaments. How-
ever, these works do not address the combination of diffu-
sion filter techniques with the interpretation of the image as
a graph, nor the parallelization of the proposed methods.
The work reported in this paper describes two parallelized
image processing methods with new preprocessing phase to
increase the detection rate of the Sun filaments. Specifically,
we use diffusion filter techniques and morphological opera-
tors to increase the detection rate or the significance of the
filaments detected. We also demonstrate that, when high
performance computing techniques are used, we can achieve
a high throughput and thus decrease the time needed to
detect filaments.
The rest of the paper is organized as follows: Section 2 des-
cribes the algorithm used to detect the filaments and diffu-
sion filter used for preprocessing; morphological techniques
are described in Section 3; the methods used to decrease the
processing time are described in Section 4; Section 5 presents
the results obtained; and finally, Section 6 shows the final
remarks.
2. FILAMENTS DETECTION AND DIFFU-
SION FILTER
The filament detection algorithm used in this work was
already described in [3]. We improve this method by adding
a preprocessing step comprising of a diffusion filter and a
post processing step to associate different gray shades for
every filament. Both steps, as well as the filament detection
algorithm, use hybrid parallel programming approach. The
entire method, called Filament Diffusion-Detection (FDD),
is depicted in Figure 2. Gray boxes in Figure 2 indicate the
added steps.
Figure 2: FDD diagram.
The FDD method comprises a preprocessing step using a
diffusion filter and a categorization of filaments. The seg-
mentation procedure consists in applying a threshold in or-
der to segment the filaments. This threshold is used in “Bi-
narization” step in Figure 2 and is the half of the average pi-
xels intensity [3]. The threshold determines if a pixel should
42
be 0, when the pixel value is less than the threshold, or 1,
when the pixel value is equal or greater than the threshold.
The filaments present themselves as dark areas in the Sun on
Hα images, since they have lower temperatures than those
from the surface of the Sun, indicated by darker pixels.
The next step (“Filament detection” depicted in Figure 2
and described in [3]) is executed to visit the pixels resulting
from the thresholding operation. For each pixel, its spatial
neighbors are visited. If such pixels are connected, they
are considered on the same filament until there are no more
neighbors. When we implemented the algorithm, we used
a circular adjacency method due to the nature of filaments.
Besides the threshold for binarization, there are two other
thresholds. One of them determines the minimum size of the
filament. The other defines a minimum distance, whenever
such filaments are considered as one.
Another step added is the association of different gray
shades for every filament, to provide an easy visualization
for each filament.
To avoid noise in preprocessing it is possible to apply a
median filter or a Gaussian filter. However, the edges of the
filaments will also be mitigated. As a result, the hit rate,
i.e. the number of correctly detected solar filaments in the
image, may also decrease.
2.1 Diffusion filter
In the filaments segmentation process, it is important that
the borders are distinct and the other areas are homoge-
neous. The Gaussian filter or the median filter can dete-
riorate the borders. To mitigate this problem we use the
diffusion filter.
As the graph theory is a well-established field, with many
algorithms to solve various problems, we can represent an
image as a graph. By combining diffusion with the interpre-
tation of an image as a graph, we can smooth the interior of
objects and still maintain the edges. To represent images as
graphs, we consider the pixels as the vertices, and the edges
are the connections, considering relative positions of image
or the properties per pixel, such as brightness. The basis of
this diffusion filter was obtained from Image Transformation
Forest [2].
To calculate which vertices are connected by edges, we can
use the relative position between vertices, as in Equation 1
and 2. Where p is the pixel and q is the adjacent pixel to
p; d(p, q) is the distance between both pixels; and t is a
threshold to delimit how much q is adjacent to the p. This
distance can be spatial or parametric.
(p, q) is an edge iff d(p, q) <= t (1)
if (p, q) is an edge , (q, p) is also an edge (2)
The diffusion filter uses a circular adjacency. Figure 3
demonstrates how this neighborhood is defined starting from
a given pixel (the brighter central pixel). The Euclidean
distance was used to calculate the distance between pixels,
and, based on it, to choose which neighbors are parts of the
adjacency and to check the distance between filaments.
Given these neighbor pixels, we only used the k-nearest
pixels, based on a parametric distance. The value of this
distance is given by the difference between the absolute value
of the adjacent pixel, i.e. luminous intensity, and the value
of the central pixel. Note that choosing the k-nearest pixels
requires the array to be sorted.
 After transforming the binary image with a threshold that
is half the average [3] of the pixels intensity (the “Binariza-
tion” phase in Figure 4), a set of morphological operators are
recursively applied in the binary image (the “Morphological
closing - set of structural elements” phase in Figure 4). This
set of operators is described in [11] and already used for the
detection of solar filaments. Figure 5 shows one sample of
this structuring element.
Figure 3: Circular pixels neighbourhood.

After the sorting of the distance vector, we do a convolu-

tion using only the k-nearest pixels, as depicted in Equation
3.

X
k
J[xp , yp ] = w[i]I[xp + dx[i], yp + dy[i]]. (3)
i=0

The convolution of the nearest pixels is done with a Gauss- Figure 5: Example of the structuring element used
ian kernel (w), using the original image (I) to produce the [11].
processed image (J). To generate the Gaussian filter coeffi-
cients, we travel the adjacency from pixel p to each of dis- Figure 8 depicts an example of the preprocessing filter
placements dx and dy which generate the q adjacent pixel, applied. The Sun image has less variation. Thus, the bina-
using the σ as the variance, applying the Equation 4. rization phase can be performed with more precision. How-
ever, some areas of the filament are obliterated by the smooth-
  ing process. The final result of the MD method is in Figure
−(|dx + dy|2 )
w(q − p) = exp . (4) 9.
2σ 2
An example of a result produced by the diffusion filter is
depicted in Figure 6. We can observe that the image is more
homogeneous, but its borders are well defined. In Figure 6,
a filament is detached for a better view.
Figure 7 presents the result of a categorization using FDD
method, after the “Diffusion Filter”, “Binarization”, “Fila-
ment detection” and the “Filament colorization” described
in Figure 2. Using this method, it is possible to observe
different gray shades for each filament.

3. MORPHOLOGICAL OPERATORS
The Morph Detection (MD) method is based on morpho-
logical operators. Mathematical morphology is applied to
image processing in many areas [4]. The diagram in Figure Figure 6: Sun image processed by the diffusion filter
4 describes the method. Gray box in Figure 4 indicates the with a manually detached filament.
added phase.

Figure 4: Diagram of the MD method.

We use two morphological operations in the MD method.

The first is a preprocessing step, called “Morphological clos-
ing - Gray Image” phase in Figure 4, where we run the
parallel morphological closing, which uses the structuring
element to perform a morphological erosion and dilatation
[4]. This morphological closing is executed four times in the
gray scale image to erase small holes in it. We have used a
structuring element with an area of 11 × 11 pixels, where all
elements are 1. Figure 7: Sun image with its categorized filaments
by the FDD method.

43

Figure 8: Sun image processed by the preprocessing
filter of the MD method with a manually detached
filament.
Figure 9: Sun image with its detected filaments by
the MD method.
4. PARALLEL PROGRAMMING TECHNI-
QUES FOR HYBRID SYSTEMS
Given the image sizes and their data volumes, it is impor-
tant to use high performance computing methods to reduce
the overall processing time. For example, for a single image
from the Big Bear Observatory collection, the sequential de-
tection of filaments using FDD method can take up to 47
minutes. In this work, we merge parallel programming tech-
niques for hybrid systems, i.e. systems that are a combi-
nation of shared and distributed memory architectures. We
use OpenMP for shared memory parallel programming and
the Message Passing Interface (MPI) library for distributed
memory parallel programming.
In a shared memory scenario, the image must be divided
in segments in order to apply the filters and other related
processes within different threads. Therefore, the image can
be divided into latitude segments of equal length, one for
each MPI process. Eventually, a small intersection area is
sent to the processes to provide pixel information in algo-
rithms that use neighbor pixels.
Figure 10 shows a diagram that describes the parallel
application. In the first step, the application reads the
image and some parameters for running. Then, it analy-
ses the image headers to define the strategy to divide the
image, with the intersection area for each MPI process if it
is needed.
44
After that, it splits the image and sends each slice to the
corresponding MPI process, using messages exchange; each
slice is further processed using OpenMP.
Finally, it rebuilds the final image, detects the filaments
split and writes the image on the hard disk. To detect the
filament split, we have to consider that, when one filament
has pixels in two different MPI processes, those pixels should
belong to a single filament.
Figure 10: Application diagram.
Astronomical images have different values for quantiza-
tion (bits per pixels), resolution and attached information.
Astronomical image quantization could be the traditional 8
bits per channel, 32 bits per channel or even 64 bits per chan-
nel. Notice that a regular image has 3 channels - Red, Green
and Blue (RGB). This diversity of quantization bits is due to
equipment that generates astronomical images. These hard-
ware are more sensible to detect different amount of light in
high spatial resolutions.
The attached information in astronomical images is very
important to describe where this image is generated, to in-
form the observed astronomical object, to capture light fre-
quency - since some events can only be registered in a par-
ticular light frequency - etc.
Therefore, in the first step, it is necessary to use an image
format that supports the richness and the great variation of
astronomical images. The format used in our system is the
Flexible Image Transport System (FITS) [7]. The FITS is a
dedicated image format endorsed by National Aeronautics
and Space Administration (NASA) and International Astro-
nomical Union (IAU) to store astronomical images.
 In the step called “analyze the image header”, image fea-
tures such as bits per pixels, width and height are extracted.
In the “Split image” step, calculations are made to define the
size of segment, the segmentation gap according to the filter
to be applied (notice the white stripes in Figure 11) and to
define which area should be processed (since the gap areas
are shared between two adjacent MPI processes). After this
step, the segments and their information are sent to a pro-
cess node using MPI.
Figure 11 shows an example where we use four MPI pro-
cesses. Each rectangle represents an area of operation for an
MPI process, while the white stripes depict the overlapping
border regions for each segment; these overlapping regions
should be sent to both processes that share the border. This
overlapping is required for processing image techniques that
use the neighborhood pixels [4], and this is a common op-
timization needed for minimizing the number of messages
between the MPI nodes.
Figure 11: Image areas attributed for each process
MPI.
On shared memory systems, in the “Process node” step
depicted in Figure 10, each OpenMP thread computes a dif-
ferent pixel on each iteration. The threads work by demand,
i. e. they process different sets of pixels, one pixel after an-
other.
After the “Process nodes” step, when all MPI processes
finish their work, they send their own slice of the processed
image to the main line to rebuild the whole image. The step
“Rebuild image” receives and regroups the images segments.
In this step, the gap information which was used for the
neighborhood process (the white stripe in Figure 11) is not
considered for the rebuild process.
An additional step is used to determine if two different fi-
laments should be considered as one. Notice the “Detecting
the continuity of filament” phase in Figure 10. This phase
is performed to check if the border pixels in adjacent image
segments have a filament in common, i.e. if they share bor-
ders in the MPI process area. Thus, if one segment has a
filament in the segment limits, it is checked if his adjacent
segment also have a filament.
The last step is the “Save image”, which writes the final
image in the FITS format.
45
In addition to the division of the image between the MPI
tasks, the program calculates the distance between each
point and the Sun center point. If this distance is greater
than a threshold, the point is not processed. This kind of
calculation is possible in this scenario because the Sun al-
ways appears in the same position in different images.
5. RESULTS
The cluster used in the tests is equipped with 5 nodes,
each of them with four 3.0 GHz Power 720 processor (each
node with 32 cores), 12 gigabytes of RAM and an Infiniband
network to interconnect the nodes. It uses AIX 6.1 operat-
ing system, IBM XL C compiler version 1.11, MPI library
version 2.1, OpenMP version 3.0 and the CFITSIO version
3.29 [6].
We used five images produced by the Big Bear Obser-
vatory for tests. Such images of the Sun were obtained in
January 2012. For each image, we manually built a “ground
truth” image, where we marked the area of each filament
with white dots, and we have used these images as refer-
ences. Figure 12 shows an example of a ground truth image.
Figure 12: Ground truth test image used for result
analysis.
In our tests, we checked how many white dots the system
categorized correctly or not. When we found an error, it
is evaluated whether it was a false positive (FP) or a false
negative (FN). A FP occurs when the detection method -
MD or FDD - indicates a filament point and the ground
truth classifies it as non-filament point. On the other hand,
a point is marked as FN when the detection method - MD
or FDD - indicates a non-filament point and the ground
truth classifies it as a filament point. In a second test, we
checked if at least one point of the filament is detected by
the method.
In the FDD method, the diffusion filter used a circular ad-
jacency with 13 pixels radius, using up to 300 closest pixels
to perform the filtering. In the detection step, within the
FDD method, the filaments should have a minimum of 20
pixels. Notice that two sets of pixels should be considered
as one filament if they have at most 100 pixels of spatial
distance. These values were empirically obtained by sam-
pling the test images. If the circular adjacency radius has
a greater value, the filter will use more pixels to calculate
the smoothing. However, in this case, adjacent pixels which
may not be related will be considered in convolution. On the
other hand, if the circular adjacency radius is lower than 13
pixels, the pixel that will receive the result of convolution
will not be as similar to its neighbors. In practice, this pro-
cedure will not soften the image.
 In 70% of the cases where a filament appears in the Sun,
a CME occurs [5]. CME is a cause of Solar Storm. In this
sense, a method which can detect filaments close to this
percentage may be considered an effective method.
Table 1 contains the hit rate of each processed image, as
well as the rates of false negatives (FN) and false positives
(FP), when comparing with the ground truth. A 100% hit
occurs when the image processed by any method is equal to
the ground truth.

Table 1: Results of detections in algorithms com-

paring every point against ground truth

FDD MD
Hits FN FP Hits FN FP
Image 1 78% 21% 1% 50% 50% 0%
Image 2 72% 24% 4% 57% 41% 2%
Image 3 83% 16% 1% 58% 42% 0%
Image 4 87% 10% 3% 56% 40% 4%
Image 5 80% 17% 3% 70% 29% 1%
Figure 13: Time used to process the FDD method
using 4, 8, 32 e 64 OpenMP threads.
The average accuracy of the FDD method is 80% with a
variation coefficient of 7%. The false negative mean in the
FDD method was 17%, the false positive was 2%. According with Figure 13, using 1 to 3 nodes the per-
The mean accuracy of MD method was 58% with a varia- formance with 64 OpenMP threads (the line with ×) or
tion coefficient of 14%. The false negative mean in the MD 32 OpenMP threads (the line with 4) are better than 8
was 40% and the false positive was 1%. OpenMP threads (the line with ). However, when more
Table 2 contains the hit rates for each processed image, than 3 nodes are used the performance of 8 OpenMP threads
considering that at least one point of the filament is detected. is better than 32 or 64 OpenMP threads.
Figure 14 shows one case, using 4, 8, 32 and 64 OpenMP
Table 2: Results of detections in algorithms con- threads per MPI process, using 1 to 5 nodes for MD method.
sidering that at least one point of the filament is
detected

Filament amount FDD FDD% MD MD %

Image 1 7 6 85% 4 57%
Image 2 11 11 100% 6 54%
Image 3 8 7 87.5% 5 62%
Image 4 7 7 100% 6 86%
Image 5 8 8 100% 6 75%

The average accuracy of the FDD method is 94% with

a variation coefficient of 1.8%. The mean accuracy of MD
method was 66% with a variation coefficient of 1.2%.
In both methods, the tests were done with 8 MPI pro-
cesses in each node and with 8 OpenMP threads for each
MPI process, in each node. To define the optimal num-
ber of processes and threads, several tests were made with
the following configurations: using 8 MPI processes and 4
OpenMP threads for each process, in each node; using 8
MPI processes and 32 OpenMP threads for each process, in
each node; and 8 MPI processes and 64 OpenMP threads
for each process, in each node. Figure 14: Time used to process the MD method
Figure 13 shows the time to process an image using 4, 8, using 4, 8, 32 e 64 OpenMP threads.
32 and 64 OpenMP threads per MPI process, using 1 up to
5 nodes for FDD method.

46
 Figure 14 shows that the performance using 32 OpenMP
threads (the line with 4) is better than 4, 8 and 64 OpenMP
threads, when we use up to 3 nodes. However, when 4 or
5 nodes are used the performance of 8 OpenMP threads is
better than with 4, 32 or 64 OpenMP threads.
The behavior presented in Figures 13 and 14 is propor-
tional to the size of the image segment that each MPI pro-
cess receives to compute. If the received segment is large,
the OpenMP threads could process with a better parallelism.
However, when the image segment is small the OpenMP
threads creation will imply in more overhead.
The graphics in Figure 14 shows the average time to pro-
cess the five images with the FDD method when using 1 to
5 nodes to compute each image. Each node hosts 8 MPI
processes, with 8 OpenMP threads for each process. When
a single thread was used, the FDD method was executed
for 47 minutes. Therefore, the FDD method obtained a 326
times speed-up with 5 nodes.
The speed-up was calculated considering the execution
time when the program uses one single thread and the ex-
ecution time when the program uses all the 5 nodes. Each
node with 8 MPI processes and each MPI process with 8
threads.
Figure 15: Time used to process the FDD method.
The graphics in Figure 16 shows the average time to pro-
cess the five images with the MD method when using 1, 2,
3, 4 and 5 nodes to compute each image. Each node uses 8
MPI processes and 8 OpenMP threads each. When a sin-
gle thread was used, the MD method was executed for 75
seconds. It means that MD method obtained a 54 times
speed-up with 5 nodes.
Figure 16: Time used to process the MD method.
47
We note that both methods can detect or, at least, in-
form the existence of the filaments, despite the considerably
variation on hit rates.
The FDD method has a set of parameters (e.g. pixels
radius, closest pixels number) that should be configured, so
the detection is made according to the user needs. The MD
method, on the other hand, has to configure the structuring
elements.
Therefore, the MD method could be used to evaluate
whether there are filaments in the Sun and if they are oc-
curring at a high rate. The FDD method, in turn, can be
used for the categorization of filaments.
6. CONCLUSION
Solar filaments are important because they are strong re-
lated to CME occurrences. In this paper, we showed two
detection methods and a parallel solution for hybrid shared
and distributed memory architectures to improve the per-
formance of the detection method.
Detecting them in traditional sequential programming is
slow because the huge data in images. These data may be
the image resolution, image quantization or other features.
In FDD method, we achieve 326-fold speed-up over with
80% hit rate (comparing pixels by pixels with the ground
truth) and a 94% accuracy (comparing if the filament is
detected) on a 5-node cluster. In the MD method, a 54-fold
speed-up was achieved with 58% hit rate and a 66% accuracy
on a 5-node cluster.
The number of OpenMP threads should consider the size
of each image segment to be processed. When the number
of segments increases the segment size decreases. Therefore,
the number of OpenMP threads should be proportional to
the size of segment, in order to minimize the process context
switch and the time for thread creation. We should highlight
that the number of OpenMP threads should be proportional
to the number of cores within the processor. Also, the num-
ber of MPI processes should be the same number of nodes
in the cluster.
For the future, we will work on improving the proposed
solution for detecting other Sun features, using other kind of
images (like extreme ultraviolet or far ultraviolet), in several
frequencies. We are targeting Sun features like sunspots,
faculae, and flares.
Moreover, we will make more tests with different ratios
between memory bandwidth, memory sizes, number of pro-
cesses and number of threads per process should be made to
determine the overall scalability of the system.
7. ACKNOWLEDGEMENTS
The authors gratefully acknowledge the financial support
from CAPES for providing the grant for the first author;
and from FAPESP projects 2010/50646-6 and 2011/00861-
0 for providing computing and research facilities. Also, the
authors acknowledge the Big Bear Solar Observatory at New
Jersey Institute of Technology, for the images; and Ph.D.
Ana Lucia Varbanescu, for the comments in this paper.
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