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Compression of triangulated solids’ surfaces by Decimating Reconstructable Triangles 通过抽取可重构三角形压缩三角化固体的表面
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102179
B. Repnik, B. Žalik, K. Rizman Žalik
{"title":"Compression of triangulated solids’ surfaces by Decimating Reconstructable Triangles","authors":"B. Repnik,&nbsp;B. Žalik,&nbsp;K. Rizman Žalik","doi":"10.1016/j.softx.2025.102179","DOIUrl":"10.1016/j.softx.2025.102179","url":null,"abstract":"<div><div>This paper introduces a new programming solution for reducing the size of files needed to store 3D geometric solids, whose surfaces are interpolated by watertight irregular triangle meshes. Unlike other approaches, the software does not introduce any special storage data format, but, instead, utilises popular CAD formats such as STL, OBJ, or PLY. This increases the software’s interoperability significantly. The software comprises an encoder and a decoder. The encoder estimates which facets may be removed in such a way that they can later be reconstructed unambiguously by the decoder. The decoder also ensures that the reconstructed triangles are oriented correctly. The encoder and the decoder are straightforward to understand and to implement. They are asymmetric, making any potential programming error easier to identify and correct.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102179"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews LitOrganizer：自动化科学文献综述的数据提取和组织过程
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102198
Alperen Şahin , Burak Can Kara , Taşkın Dirsehan
{"title":"LitOrganizer: Automating the process of data extraction and organization for scientific literature reviews","authors":"Alperen Şahin ,&nbsp;Burak Can Kara ,&nbsp;Taşkın Dirsehan","doi":"10.1016/j.softx.2025.102198","DOIUrl":"10.1016/j.softx.2025.102198","url":null,"abstract":"<div><div>Scientific literature reviews have become a time-consuming and complex process due to the increasing volume of data. Manual data extraction and organization significantly hinder the efficiency of this process. LitOrganizer, a Python-based software, assists researchers by scanning PDF files with specified keywords and consolidating the extracted information into a Word document, including the source name and page number where the information appears. Additionally, it identifies the DOI numbers of files, renaming the documents with the correct citation information, and helps organize both the PDF documents and the specific data efficiently.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102198"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A computerized tool for the kinematic limit analysis of 2D masonry structures failing on a tilting table 倾斜台上二维砌体结构运动极限分析的计算机化工具
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102180
Yiwei Hua, Martina Buzzetti, Natalia Pingaro, Luis C.M. da Silva, Gabriele Milani
{"title":"A computerized tool for the kinematic limit analysis of 2D masonry structures failing on a tilting table","authors":"Yiwei Hua,&nbsp;Martina Buzzetti,&nbsp;Natalia Pingaro,&nbsp;Luis C.M. da Silva,&nbsp;Gabriele Milani","doi":"10.1016/j.softx.2025.102180","DOIUrl":"10.1016/j.softx.2025.102180","url":null,"abstract":"<div><div>A Limit Analysis computer Code for masonry walls collapsing in Tilting Table Tests (LACT<sup>3</sup>) is presented. Specifically, LACT<sup>3</sup> is a MATLAB®-based graphical user interface useful to determine the ultimate load-bearing capacity of masonry walls in-plane loaded. The latter are modelled within a heterogeneous approach where blocks are assumed infinitely resistant and joints are reduced to interfaces exhibiting an associated rigid-plastic behaviour, ruled by a Mohr-Coulomb failure criterion. At incipient collapse, the mechanical problem can be therefore described by means of the two classic limit analysis theorems. LACT<sup>3</sup> extracts the geometry of the masonry wall directly from a dxf file, with a precise description of block dimension and shape. The upper bound theorem of limit analysis is used, and the collapse tilting angle is determined along with the corresponding failure mechanism, recursively solving a linear programming problem at progressively increased values of rotation of the tilting table. Additionally, the self-dual linear programming approach enables the evaluation of internal actions. The proposed tool is highly user-friendly, requiring only a basic knowledge of CAD software, and is easily manageable as it requires only two mechanical parameters for the joints: (i) friction angle and (ii) cohesion. LACT<sup>3</sup> provides an efficient means for the rapid assessment of 2D masonry structures under horizontal loads.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102180"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
3PB-analyzer: A python-based tool for automated three-point bending analysis 3pb分析仪：基于python的自动三点弯曲分析工具
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102177
Yutao He, Xiaodie Fan, Xi Li, Rui Cheng, Bin Wang
{"title":"3PB-analyzer: A python-based tool for automated three-point bending analysis","authors":"Yutao He,&nbsp;Xiaodie Fan,&nbsp;Xi Li,&nbsp;Rui Cheng,&nbsp;Bin Wang","doi":"10.1016/j.softx.2025.102177","DOIUrl":"10.1016/j.softx.2025.102177","url":null,"abstract":"<div><div>This paper presents 3PB-Analyzer, an open-source Python-based software tool developed to simplify and enhance the analysis of three-point bending test data. Three-point bending is a widely used experimental method for evaluating the mechanical properties of materials, such as stiffness, strength, and fracture toughness. In biomechanics, it plays a crucial role in assessing bone quality, understanding the impact of diseases or treatments, and studying material behavior under loading conditions. Despite its significance, many existing data analysis tools are limited in accuracy, flexibility, and ease of use. 3PB-Analyzer addresses these challenges by automating key steps, including locating and importing raw CSV files, generating load-displacement scatter plots, and performing linear regression analysis to calculate critical parameters such as stiffness, yield force, post-yield displacement, and work-to-fracture. Designed for researchers with or without programming expertise, the tool features an intuitive graphical user interface (GUI) that ensures accessibility and ease of operation. Although tailored for bone biomechanics, the 3PB‑Analyzer can be applied to three‑point bending experiments on any material and is fully compatible with four‑point bending tests as well. By combining precision, automation, and versatility, this tool enables researchers to streamline data processing, improve analytical accuracy, and enhance the reproducibility of their results, making it a valuable resource across multiple disciplines.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102177"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143895654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TMEImmune: A Python Package for deriving prognostic tumor micro-environment score TMEImmune：用于获得预后肿瘤微环境评分的Python包
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102169
Q. Zhou, L. Shahriyari
{"title":"TMEImmune: A Python Package for deriving prognostic tumor micro-environment score","authors":"Q. Zhou,&nbsp;L. Shahriyari","doi":"10.1016/j.softx.2025.102169","DOIUrl":"10.1016/j.softx.2025.102169","url":null,"abstract":"<div><div>Immune checkpoint inhibitor (ICI) therapy has become a powerful tool in cancer treatment in recent years. However, due to its limited response rate, there is an urgent need for computational methods to accurately predict patient response. We therefore developed the Python package TMEImmune, which integrates four widely used prognostic scoring methods for ICI therapy. This package allows users to easily compare the performance of these methods across various cancer types, helping to identify the most predictive approach for each cancer.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102169"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
KHNN: Hypercomplex-valued neural networks computations via Keras using TensorFlow and PyTorch KHNN：使用TensorFlow和PyTorch通过Keras进行超复杂值神经网络计算
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102163
Agnieszka Niemczynowicz, Radosław A. Kycia
{"title":"KHNN: Hypercomplex-valued neural networks computations via Keras using TensorFlow and PyTorch","authors":"Agnieszka Niemczynowicz,&nbsp;Radosław A. Kycia","doi":"10.1016/j.softx.2025.102163","DOIUrl":"10.1016/j.softx.2025.102163","url":null,"abstract":"<div><div>Neural networks that utilize algebras more advanced than real numbers, such as hypercomplex numbers, can outperform traditional models in certain applications, usually, in the number of training parameters giving the same accuracy. However, no general framework exists for constructing hypercomplex neural networks. We propose a library integrated with Keras, TensorFlow, and PyTorch, enabling computations within these advanced algebraic systems. The library offers Dense and Convolutional layer architectures for 1D, 2D, and 3D data, tailored to support hypercomplex operations. This tool provides a streamlined approach for developing models that leverage hypercomplex numbers, enhancing performance in areas like image processing and signal analysis, and fostering innovation in machine learning. The branch of this software – HypercomplexKeras – is the Keras extension for hypercomplex neural networks.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102163"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143948742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Surgical planning for brain intervention (SPBI) using multimodal brain MR images 应用多模态脑MR图像进行脑介入手术计划
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102197
Yi Zhang , Zhao He , Shijie Hong , Fulang Qi , Qingfang Sun , Guang-Zhong Yang , Yuan Feng
{"title":"Surgical planning for brain intervention (SPBI) using multimodal brain MR images","authors":"Yi Zhang ,&nbsp;Zhao He ,&nbsp;Shijie Hong ,&nbsp;Fulang Qi ,&nbsp;Qingfang Sun ,&nbsp;Guang-Zhong Yang ,&nbsp;Yuan Feng","doi":"10.1016/j.softx.2025.102197","DOIUrl":"10.1016/j.softx.2025.102197","url":null,"abstract":"<div><div>Interventional MRI (i-MRI) has been used for improving the accuracy and safety of brain intervention. The surgical navigation system that provides guidance before and during the intervention is crucial for the operation, especially for robot-assisted neurosurgery. Here we present a Surgical Planning for Brain Intervention (SPBI) software system. SPBI provides a series of functionalities to improve the safety and precision of brain intervention, including brain tissue segmentation, vessel segmentation, fiber tracking, and intervention path planning. Multimodal brain MR images from healthy volunteers were used for demonstration of the functionalities. Codes and sample data are open-sourced and publicly available.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102197"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DigiRhythm: An R package for evaluating circadian rhythmicity in animals using the degree of functional coupling DigiRhythm：一个用功能耦合程度来评估动物昼夜节律性的R软件包
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102184
Hassan-Roland Nasser , Marianne Cockburn , Marie Schneider
{"title":"DigiRhythm: An R package for evaluating circadian rhythmicity in animals using the degree of functional coupling","authors":"Hassan-Roland Nasser ,&nbsp;Marianne Cockburn ,&nbsp;Marie Schneider","doi":"10.1016/j.softx.2025.102184","DOIUrl":"10.1016/j.softx.2025.102184","url":null,"abstract":"<div><div>Studying animals’ rhythmicity provides insights into their physiological and psychological states. The degree of functional coupling (DFC) is one of the algorithms available to assess rhythmicity in activity-related time series data, such as accelerometer or GPS data. However, DFC computation is complex, as it includes frequency spectrum analysis and statistical significance testing. This paper introduces digiRhythm, an R package that makes the DFC-based rhythmicity analysis easily accessible. Beyond the DFC, the package includes an additional set of tools, which are crucial for rhythmicity investigations, such as actogram generation, daily activity visualization, and diurnality index computation.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102184"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143936600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Update 2.0 to Coastal dynamics analyzer (CDA): A QGIS plugin for transect and area based analysis of coastal erosion 更新2.0海岸动态分析仪（CDA）：一个QGIS插件，用于基于样带和区域的海岸侵蚀分析
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102170
Pietro Scala , Giorgio Manno , Carlo Lo Re , Giuseppe Ciraolo
{"title":"Update 2.0 to Coastal dynamics analyzer (CDA): A QGIS plugin for transect and area based analysis of coastal erosion","authors":"Pietro Scala ,&nbsp;Giorgio Manno ,&nbsp;Carlo Lo Re ,&nbsp;Giuseppe Ciraolo","doi":"10.1016/j.softx.2025.102170","DOIUrl":"10.1016/j.softx.2025.102170","url":null,"abstract":"<div><div>The Coastal Dynamics Analyzer (CDA) v.2.0 is an enhanced version of the existing QGIS plugin, CDA v.1.0, which was originally developed for transect-based analysis (TBA) in coastal erosion assessment. This new release introduces the Area-Based Analysis (ABA), a new methodology useful for analyzing irregular or dynamic shorelines. By integrating ABA, CDA v.2.0 enables users to evaluate broader coastal dynamics and changes, providing a more comprehensive toolkit for researchers and professionals engaged in coastal monitoring and management. The plugin maintains its user-friendly interface and compatibility with QGIS, ensuring seamless integration into existing workflows.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":"Article 102170"},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TeamPlus: A data-driven tool utilizing a Genetic Algorithm for optimal software team formation TeamPlus：一个数据驱动的工具，利用遗传算法来优化软件团队的形成
IF 2.4 4区 计算机科学
SoftwareX Pub Date : 2025-05-01 DOI: 10.1016/j.softx.2025.102174
Felipe Cunha, Mirko Perkusich, Danyllo Albuquerque, Kyller Gorgônio, Hyggo Almeida, Angelo Perkusich
{"title":"TeamPlus: A data-driven tool utilizing a Genetic Algorithm for optimal software team formation","authors":"Felipe Cunha,&nbsp;Mirko Perkusich,&nbsp;Danyllo Albuquerque,&nbsp;Kyller Gorgônio,&nbsp;Hyggo Almeida,&nbsp;Angelo Perkusich","doi":"10.1016/j.softx.2025.102174","DOIUrl":"10.1016/j.softx.2025.102174","url":null,"abstract":"<div><div>TeamPlus is a data-driven tool designed to optimize software team formation. By integrating with project management systems, it leverages data analytics to create detailed profiles and suggest optimal team configurations, allowing for managerial adjustments. We implemented this tool using a Genetic Algorithm (GA) with Convex Combination Crossover and validated it through two approaches: an experiment comparing our GA with traditional methods (i.e., Partially Mapped Crossover and One-Point Crossover) using data from 47 projects and 149 developers, and an evaluation of fifteen features by an industry expert, comparing them with tools from six recent studies. Our GA significantly outperformed traditional crossover methods, and TeamPlus offers a more comprehensive and flexible set of features, improving decision-making efficiency and team formation quality.</div></div>","PeriodicalId":21905,"journal":{"name":"SoftwareX","volume":"30 ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143927641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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