Review of the Software Packages for Estimation of the Fractal Dimension
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ICT Innovations 2015 Web Proceedings ISSN 1857-7288 Review of the Software Packages for Estimation of the Fractal Dimension Elena Hadzieva1, Dijana Capeska Bogatinoska1, Ljubinka Gjergjeska1, Marija Shumi- noska1, and Risto Petroski1 1 University of Information Science and Technology “St. Paul the Apostle” – Ohrid, R. Macedonia {elena.hadzieva, dijana.c.bogatinoska, ljubinka.gjergjeska}@uist.edu.mk {marija.shuminoska, risto.petroski}@cse.uist.edu.mk Abstract. The fractal dimension is used in variety of engineering and especially medical fields due to its capability of quantitative characterization of images. There are different types of fractal dimensions, among which the most used is the box counting dimension, whose estimation is based on different methods and can be done through a variety of software packages available on internet. In this pa- per, ten open source software packages for estimation of the box-counting (and other dimensions) are analyzed, tested, compared and their advantages and dis- advantages are highlighted. Few of them proved to be professional enough, reli- able and consistent software tools to be used for research purposes, in medical image analysis or other scientific fields. Keywords: Fractal dimension, box-counting fractal dimension, software tools, analysis, comparison. 1 Introduction The fractal dimension offers information relevant to the complex geometrical structure of an object, i.e. image. It represents a number that gauges the irregularity of an object, and thus can be used as a criterion for classification (as well as recognition) of objects. For instance, medical images have typical non-Euclidean, fractal structure. This fact stimulated the scientific community to apply the fractal analysis for classification and recognition of medical images, and to provide a mathematical tool for computerized medical diagnosing. We bring up to the attention that, throughout the papers we have analyzed, and the software tools we have examined, there is a significant inconsistency among the au- thors, concerning the dimension’s terminology. Sometimes the box-counting dimen- sion is called the Hausdorff dimension or the similarity dimension is called the box counting dimension. Here we will give only the definitions of fractal and box-counting fractal dimensions. 201 S. Loshkovska, S. Koceski (Editors): ICT Innovations 2015, Web Proceedings, ISSN 1857-7288 © ICT ACT http://ictinnovations.org/2015, 2015 ICT Innovations 2015 Web Proceedings ISSN 1857-7288 Definition by Barnsley [1]. Given 휀 > 0. Let 푁(휀) be the smallest number of closed balls of radius 휀>0 needed to cover the set F. The fractal dimension of the set F is the number ln(푁(휀)) 퐷(퐹) = 푙푖푚 (1) 휀→0 ln 휀 A theorem stated in [1] states that if instead of closed balls, boxes of side length 1/2n are used, the fractal dimension of the set F, D(F), is equal to the number ln(푁(푛)) 퐷 (퐹) = 푙푖푚 (2) 퐵 푛→∞ ln 2푛 where N(n) is the number of boxes that have nonempty intersection with the set F. DB(F) is usually referred to as the box-counting fractal dimension of the set F. The software tools that we have analyzed, mainly compute the box-counting dimen- sion by the basic box-counting method, described by the equation (2). (Practically, the image is covered with the boxes of side length 1/2i, where i is a positive integer that has appropriately chosen maximum value n. Then, the approximation of the limit from the definition is the slope of the line that fits the finite set of data {(log2i, logN(i)) | i = 1, 2,…, n, n is a finite number}). Falconer in [6] gives excellent clarification of the different types of the dimensions. The fractal approach in medical diagnostics is noted as reasonable and many times reported in papers [9], [16], [14], [12], [13], [10]. The authors encounter many problems related to the image analysis, like: having images with different resolution (which af- fects the fractal dimension), the brightness-contrast enhancement of the imaging device, the expertise of the person that collects the images, the presence of noise, masking structures, the variability of shapes and tissues, ([4]; [15]). Additionally, they encoun- ter problems related to the fractal analysis: which software tool will be the most com- patible for their research, which type of the dimension will quantify the best their sub- jects of research, which method for estimation of particular fractal dimension to choose (if the software tool offers such options, at all), how to set the parameters included, does the tool accepts the images in particular format, and so on. Some of the ambigui- ties are detected by Lopes, Betrouni, Braverman and reported in [11], [2]. In this paper we will state the uncertainties related to the reliability of the existing software tools for estimation of the box counting fractal dimension, performed using the basic method. We will apply several software tools (will be listed later) to estimate the box-count- ing fractal dimension of three strict self-similar IFS fractals: the Sierpinski triangle, the Koch snowflake and the Minkovski sausage, and their parts, specially chosen: smaller copies of the fractal itself and one biomedical image of tinea corporis disease (see Fig. 1). 202 S. Loshkovska, S. Koceski (Editors): ICT Innovations 2015, Web Proceedings, ISSN 1857-7288 © ICT ACT http://ictinnovations.org/2015, 2015 ICT Innovations 2015 Web Proceedings ISSN 1857-7288 Fig. 1. Samples of fractals It is known (see for instance [6]) that the similarity, box counting and Hausdorff di- mensions of the Sierpinski triangle and Koch curve are equal, ln 3 DH (Sierp) = DB (Sierp) = DS (Sierp) = =1.58496 and ln 2 ln 4 DH (Koch curve) = DB (Koch curve)= DS (Koch curve) = =1.26186. ln 3 A theorem formulated in [1] can be used to show that DB (Koch snowflake) = DB (Koch curve)= 1.26186. Similarly, it can be shown that ln 8 DH (Mink. saus.)= DB (Mink. saus.)= DS (Mink. saus.) = = 1.5000. ln 4 Later (in section 3) we will compare the values of these box counting dimensions with our estimated results, so to characterize the reliability of the examined software tools. Additionally, we have decided to estimate the fractal dimensions of parts (actually smaller copies) of Sierpinski triangle and Koch curve, to check the consistency of the algorithms, since the dimensions of a self-similar fractal and its smaller copy, in ideal case, when infinite number of iterations are performed, are equal. We have used both types of black and white images: white image on black background (Minkowski sau- sage) and black image on white background (Sierpinski and Koch fractals), because some of the software tools have an option for choosing which pixels are “active”, black or white. We have also estimated the fractal dimension of a medical image, such as the image of the skin disease Tinea corporis (Fig. 1), so to test the software tools on real cases. In the remaining sections we will analyze the chosen open source available software tools used for computing the box-counting fractal dimension, test the software tools over the aforementioned strict self-similar fractals and a medical image, resume the results of testing and give the description and comparison of the tools. 203 S. Loshkovska, S. Koceski (Editors): ICT Innovations 2015, Web Proceedings, ISSN 1857-7288 © ICT ACT http://ictinnovations.org/2015, 2015 ICT Innovations 2015 Web Proceedings ISSN 1857-7288 2 Description and Analysis of the Available Software Tools The software tools illustrated in this section are based mostly on the basic method for computing the box-counting fractal dimension explained in the section 1. There are only two tools which are based on other methods and such aspect is emphasized in the description of the software tools. 2.1 FracLAC [Author: Audrey Karperien, http://rsb.info.nih.gov/ij/plugins/fraclac/FLHelp/Introduction.htm] FracLAC is an open source available plugin for ImageJ aimed for the detailed fractal analysis of images. FracLAC is also available as a standalone Java application, but the plugin is more up-to-date and has more features than standalone version. FracLAC for ImageJ is a user friendly and comprehensive toolset, widely used in many different disciplines, especially in medical image processing, in almost all medical fields: oph- thalmology and visual science, oncology, neurology, cardiology, in cancer research etc. A lot of papers from these and other scientific fields that use FracLAC are cited on its official web site. FracLAC is not only raw software for mathematical analysis, but it also contains a rich documentation explaining the concept of fractal analysis. It can be used for fractal and multifractal analysis over: entire open images, ROIs and multiple files. Images, of type jpg, tiff, png or gif, have to be opened with ImageJ. They have to be in grayscale or binary format (otherwise, conversion is necessary). Preprocessing (like thresholding, background subtraction, dilatation, edge detection) should be done in ImageJ or other image processing software. Preparation of the images depends on the aim and type of analysis and also on the type of image (grayscale or binary, contour or texture etc.). The user friendly interface offers a few options: Box-counting and Lacunarity Anal- ysis (which is analyzed within this paper), Sliding Box Lacunarity Analysis, Mass vs. Distance Analysis, Local Connected Fractal Dimension Analysis, Sub Sample and Par- ticle Analyser Analysis and Multifractal Analysis, with the possibility of setting a con- siderable number of parameters in all the aforementioned options. After reading the comprehensive explanation that is available in the interface itself, we have set the pa- rameters as if they were standards so that comparable results with other software pack- ages could be obtained (such settings are actually much below the wide web of possi- bilities offered through FracLAC).