MeshPipe: a Python-based tool for easy automation and demonstration of geometry processing pipelines

The popularization of inexpensive 3D scanning, 3D printing, 3D publishing and AR/VR display technologies have renewed the interest in open-source tools providing the geometry processing algorithms required to clean, repair, enrich, optimize and modify point-based and polygonal-based models. Nowadays, there is a large variety of such open-source tools whose user community includes 3D experts but also 3D enthusiasts and professionals from other disciplines. In this paper we present a Python-based tool that addresses two major caveats of current solutions: the lack of easy-to-use methods for the creation of custom geometry processing pipelines (automation), and the lack of a suitable visual interface for quickly testing, comparing and sharing different pipelines, supporting rapid iterations and providing dynamic feedback to the user (demonstration). From the user's point of view, the tool is a 3D viewer with an integrated Python console from which internal or external Python code can be executed. We provide an easy-to-use but powerful API for element selection and geometry processing. Key algorithms are provided by a high-level C library exposed to the viewer via Python-C bindings. Unlike competing open-source alternatives, our tool has a minimal learning curve and typical pipelines can be written in a few lines of Python code.Peer ReviewedPostprint (published version

Study: Visualization of spacecraft trajectories with NASA SPICE and Blender

Visualizing spacecraft trajectories is interesting because of its compelling applications. From educational and public divulgation purposes, to mission planning and analysis, many fields can benefit from research in this topic. This project aims to provide with a tool to visualize such trajectories in a comprehensible three-dimensional manner. For this reason, a toolkit programmed in python and integrated into Blender and using the SPICE system has been developed. On rare occasions SPICE and Blender have been integrated together. SPICE is a system created by NASA with the goal of assisting engineers and scientist in the planning and interpretation of space instruments observations, and in space exploration modeling and planning. It is a tool that analyzes data sets composed of navigation information to obtain precise observation geometry. Blender is a free and open-source 3D fully integrated 3D creation suite. It supports modeling, animation, rendering and video editing, among many other features. The toolbox developed is able to recreate scenes by retrieving location, orientation and other data from SPICE, and applying this information to the animation. All space bodies are created as instances of different classes, which consist of planets, moons, stars and spacecrafts. The Blender scene is recreated using ancillary functions and the class functions of each object, which consist of creating the different objects in the scene, applying them their texture and animating the multiple bodies at each frame. The toolkit makes use of the Blender API to access the program using its functions and classes. The in-built Blender renders Eevee and Cycles are used to obtain images and videos. The primitive mesh UV sphere is used to recreate the solar system bodies and stars, alongside materials with map textures. 3D models are used for the spacecrafts. Some examples have been recreated to illustrate the capabilities of the developed toolkit. These consist of a recreation of the iconic image “Earth rising over the Moon’s Horizon”, an animation of the inner solar system during a whole year, a comparison of the constellations viewed from the Earth, two recreations of real images taken by Cassini one depicting three Saturn moons as they orbit over the rings and the other the moon Pan inside the Encke gap, an animation of the trajectory and attitude of Cassini during the insertion into Saturn orbit, and a recreation of an image taken by Voyager 1 showing an ongoing eruption on Io. Overall, the toolkit is able to successfully recreate scenarios involving spacecrafts and their trajectories. It enables the user to comprehend the three-dimensional relative position of the bodies, and to recreate real images taken by spacecraft as well as simulate pictures that never happened. For these reasons, amongst its most important applications are education and dissemination

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the Finite Element Method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies available upon reques

Graphic Adventure videogame using Fuzzy Logic algorithms to set the path of the story

Treball final de Grau en Disseny i Desenvolupament de Videojocs. Codi: VJ1241. Curs acadèmic: 2018/2019The objective in this technical proposal is to present a Final degree project that consists on the creation of a post apocalyptic graphic adventure with alternative endings and events based on the player choices. The events and endings will not only be ordered by player choices but by a Fuzzy logic that will take on account the player actions. This project will be on 3D with an isometric view view and will be developed on Unity3D

An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries

Advances in imaging methods such as electron microscopy, tomography and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this study, we outline the steps for a na\"ive user to approach GAMer 2, a mesh generation code written in C++ designed to convert structural datasets to realistic geometric meshes, while preserving the underlying shapes. We present two example cases, 1) mesh generation at the subcellular scale as informed by electron tomography, and 2) meshing a protein with structure from x-ray crystallography. We further demonstrate that the meshes generated by GAMer are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.Comment: 6 pages and 4 figures. Supplemental Movie available upon reques