A Heuristic-Based Decision Tree for Connected Components Labeling of 3D Volumes: Implementation and Reproducibility Notes

. This paper provides a detailed description of how to install, setup, and use the YACCLAB benchmark to test the algorithms published in “A Heuristic-Based Decision Tree for Connected Components Labeling of 3D Volumes,” underlying how the parameters aﬀect and in-ﬂuence experimental results.


Introduction
Although introduced many decades ago [31], the task of labeling objects inside binary images is still employed in several scenarios, whenever an identification of segmented visual objects or image regions is required. This procedure, usually identified as Connected Components Labeling or CCL in short, has a unique and exact solution which provides a description of the objects inside binary images, represented by an output symbolic image where pixels of a connected component are assigned the same integer identifier.
As a matter of fact, many state-of-the-art image processing and computer vision pipelines exploit CCL as a fundamental pre-or post-processing step. The fields of application of such an algorithm range from Object Tracking [18] to Document Restoration [10,25], including Image Segmentation [1,29], Medical Imaging [13,19,30] and many others [6,17]. For this reason, having a fast and efficient algorithm, able to minimize its impact on image analysis tasks, is undoubtedly very advantageous. This is why the research efforts in labeling techniques have such a very long story, full of different strategies and improvements targeting both sequential [8,9,20,22,23,34] and parallel architectures [2,3,5,24,28,32,35]. Among them, some of the most promising techniques that led to major breakthroughs in the field consist in the usage of Decision Trees (DTrees), combined with the 2 × 2 block-based approach. A detailed description of the algorithms based on these paradigms is provided in [7]. Moreover, algorithmic solutions relying on DTrees have demonstrated their effectiveness even when applied, with the necessary variations, to parallel architectures [4,12].
Unfortunately, existing techniques for the generation of DTrees become quickly unfeasible when the size of the mask used to scan the input image increases. This prevented the application of block-based trees to 3D scenarios. In order to compensate for this limitation a novel heuristic algorithm, based on decision tree learning and named Entropy Partitioning Decision Tree (EPDT), has been presented in [33]. This algorithm allows to compute near-optimal decision trees for large scan masks, overtaking the limitations of existing approaches.
This paper describes the benchmark used to evaluate the performance of EPDT-generated algorithms, focusing on how to configure it to reproduce the experiments reported in [33].

The Evaluation Framework
YACCLAB, Yet Another Connected Components Labeling Benchmark, has been originally released in [21] with the aim of providing a fair comparison and evaluation of CCL algorithms. The benchmark has been later improved with additional datasets, tests and with an extension to 3D and GPU algorithms [5,11]. After its first appearance in 2016, it has been used by many authors [14,15,36] to compare the performance of novel proposals with state-of-the-art solutions, thus setting a de-facto standard.
When measuring the performance of an algorithm several details should be taken into account, as they could significantly influence the performance. However, CCL is a well-defined problem and the burden of evaluation can be reduced to the measure of execution "speed".
The main elements that affect execution speed can be resumed as follows: data on which tests are performed, implementation details, hardware capabilities, and code optimization provided by the compiler. YACCLAB takes all these aspects into account; the benchmark is open-source and provides an implementation of state-of-the-art algorithms, directly including the source code released together with the scientific papers whenever available. Given its open-source nature, anyone can verify literature claims testing the algorithms with any combination of hardware architecture, operating system and build tools.
The public dataset provided with the benchmark covers most of CCL fields of application, including 2D images and 3D volumes of both real world and synthetically generated domains. A detailed description of the YACCLAB dataset is available in [5]. Because experimental results reported in [33] concern 3D EPDTgenerated algorithms, the general properties of 3D datasets are summarized in Table 1 and a brief description follows: -OASIS is a dataset of medical MRI data taken from the OASIS project [27], binarized with the Otsu threshold; -Mitochondria is the Electron Microscopy Dataset [26], which contains binary sections taken from the CA1 hippocampus; -Hilbert consists of the 3D Hilbert curve, which is a fractal space-filling curve, obtained at different iterations (1 to 6) of the construction method.
The source code of the EPDT-generated algorithms as well as the benchmarking suite is available at https://github.com/prittt/YACCLAB.
The installation procedure is well detailed in the aforementioned GitHub repository; the main steps can be resumed as follows: -Clone the repository; -Generate the YACCLAB project using CMake; -Set the configuration file config.yaml placed in the installation folder; -Open the project folder, build and run.
When configuring the project through CMake the flags YACCLAB ENABLE 3D and YACCLAB ENABLE EPDT * must be enabled in order to set-up the benchmark for 3D algorithms and to include EPDT implementations. The CMake file should automatically find the OpenCV installation path, otherwise it must be manually specified. The flag YACCLAB DOWNLOAD DATASET 3D must be enabled if the user wants CMake to automatically download the YACCLAB 3D dataset. CMake will automatically generate the C ++ project for the selected compiler.
YACCLAB allows to perform multiple tests: correctness is an initial validation of the algorithms; average runs algorithms on every image of a dataset, measuring the average run-time; average with steps measures separated run-times for the different steps each algorithm is composed of, including multiple scans over the input image and allocation/deallocation of data structures; granularity uses synthetic images to evaluate the performance of different approaches in terms of scalability on the number of pixels, foreground density and pattern granularity; memory reports the expected number of memory accesses required by an algorithm on a reference dataset.
YACCLAB stores experimental results in the output path specified by the configuration file. Multiple output formats including plain text, bar chart and L A T E X table will be produced.
CCL algorithms are independent of the Union-Find strategy employed. For this reason YACCLAB provides a Union-Find templated implementation for most of the algorithms, thus being able to compare each algorithm (but those for which the label solver is built-in) with different label solving strategies: standard Union-Find (UF), Union-Find with Path Compression (UFPC) [34], Interleaved Rem's algorithm with splicing (RemSP) [16] and Three Table Array (TTA) [22]. This standardization reduces code variability, allowing to separate label solving data structures from CCL strategies, and provides fair comparisons without negatively impacting execution time. The EDPT algorithms were tested on an Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz with Windows 10.0.17134 (64 bit) OS and the MSVC 19.15.26730 compiler. The benchmark was compiled for x64 architecture with optimizations enabled. It is worth noticing that most compilers need several minutes to build EPDT algorithms; in particular, some of them actually fail to compile EDPT 26c. For these reasons, aforementioned algorithms are optional and must be singularly enabled with CMake, as described in Section 3.
The performance of EPDT-generated algorithms have been compared to stateof-the-art solutions over the collection of 3D datasets included in YACCLAB and described in Section 2. In order to reproduce the same experiments reported in [33], the CPU 3D 26-way connectivity section of the configuration file must have its execute, perform and algorithms fields set as in Listing 1. The other fields can remain as default. Finally, 2D tests can be disabled to avoid useless experiments.

Conclusion
We described how to reproduce the experimental results reported in [33]. The environment employed for testing the algorithms can significantly affect performance. Cache size and RAM speed can change absolute results while preserving relative performance. Operative System and compiler are likely to heavily influence the outcome.