Visualization and Sharing of 3D Digital Outcrop Models to Promote Open Science Visualization and Sharing of 3D Digital Outcrop Models to Promote Open Science

Home , Digital outcrop model, Outcrop, Photogrammetry, Sketchfab

25–28 Oct. GSA 2020 Annual Meeting

VOL. 30, NO. 6 | JUNE 2020

Paul Ryan Nesbit, Adam D. Boulding, Christopher H. Hugenholtz, Dept. of Geography, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada; Paul R. Durkin, Dept. of Geological Sciences, University of Manitoba, 66 Chancellors Circle, Winnipeg, Manitoba, R3T 2N2, Canada; and Stephen M. Hubbard, Dept. of Geoscience, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada

ABSTRACT INTRODUCTION opportunities to analyze and revisit data at High-resolution 3D data sets, such as High-resolution 3D digital models are multiple scales. Open source programs, digital outcrop models (DOMs), are increas- becoming increasingly common data sets in such as Blender and CloudCompare, can be ingly being used by geoscientists to supple- academic and commercial applications. In used for data exploration and measurement ment field observations and enable multi- the geosciences specifically, digital outcrop and have also integrated specific geosci- scale and repeatable analysis that was models (DOMs), or virtual outcrops, can ence toolsets (e.g., Brodu and Lague, 2012; previously difficult, if not impossible, to provide geoscientists with photorealistic Dewez et al., 2016; Thiele et al., 2017). achieve using conventional methods. De- models that preserve spatial precision, Although acquiring DOMs has become spite an increasing archive of DOMs driven dimensionality, and geometric relationships more straightforward, and various 3D analy- by technological advances, the ability to between geologic features that are inherently sis programs are available, dissemination of share and visualize these data sets remains 3D and susceptible to distortion and/or loss DOMs, interpretations, and results has a challenge due to large file sizes and the of information when rendered in 2D (Bellian remained a challenge due to software and need for specialized software. Together, et al., 2005; McCaffrey et al., 2005; Jones et file-size barriers. Specialty 3D programs are these issues limit the open exchange of data al., 2009). Digital 3D mapping approaches often hindered by product licensing and can sets and interpretations. To promote greater using DOMs have enabled geoscientists to involve a considerable learning curve to data accessibility for a broad audience, perform supplemental measurements, corre- understand controls, file formats, and inte- we implement three modern platforms for lations, and interpretations that are difficult grated tools. Furthermore, DOMs can easily disseminating models and interpretations or impossible to obtain with traditional meth- exceed multiple gigabytes (GB) in size, within an open science framework: Sketch- ods (Figs. 1–2; Pavlis and Mason, 2017; Nes- which can be taxing on computational fab, potree, and Unity. Web-based plat- bit et al., 2018). resources for rendering, file storage, and forms, such as Sketchfab and potree, render Until recently, however, collection and data transfer. With the growing collection of interactive 3D models within standard use of digital data sets has been limited to high-resolution DOMs and similar 3D data web browsers with limited functionality, specialists, due to hardware and software sets, there is a need for dedicated, intuitive, whereas game engines, such as Unity, limitations. A number of methods are now and accessible 3D visualization platforms. enable development of fully customizable available for collecting and processing 3D Given the challenges outlined above, we 3D visualizations compatible with multiple models (Hodgetts, 2013; Carrivick et al., examined existing visualization solutions operating systems. We review the capabili- 2016). In particular, structure-from-motion that could potentially enable sharing of ties of each platform using a DOM of an and multi-view stereo (SfM-MVS) photo- DOMs and support open science through extensive outcrop exposure of Late Creta- grammetry software, commonly paired increased data accessibility. To provide a ceous fluvial stratigraphy generated from with uninhabited aerial vehicles (UAVs), functional introduction to modern visualiza- uninhabited aerial vehicle images. Each enables geoscientists to produce photoreal- tion platforms, we illustrate the capabilities visualization platform provides end-users istic DOMs through a highly streamlined and functionality of two web-based inter- with digital access and intuitive controls to UAV-SfM workflow (Chesley et al., 2017; faces (Sketchfab and potree) and a cross- interact with large DOM data sets, without Nieminski and Graham, 2017; Pavlis and platform videogame engine (Unity) using a the need for specialized software and hard- Mason, 2017; Nesbit and Hugenholtz, 2019). geologic case study. A DOM was produced ware. We demonstrate a range of features Related efforts have centered on the through a UAV-SfM workflow for an exten- and interface customizability that can be development of 3D software solutions with sive outcrop (1 km2) exposed within the bad- created and suggest potential use cases tools for geoscience applications. Custom land landscape of Dinosaur Provincial Park to share interpretations, reinforce student software packages, such as Virtual Reality (Alberta, Canada). Each visualization plat- learning, and enhance scientific communi- Geology Studio (VRGS; Hodgetts et al., form provides access to the large DOM cation through unique and accessible visu- 2007) and LIME (Buckley et al., 2019), through an intuitive lightweight interface alization experiences. offer users lightweight executable tools and without the need for high-end hardware,

accretion w leo o 2 m paleo opa

channel-belt base oodplain mudstone channel-belt base

Figure 1. Geologic interpretations (line drawing on 2D field photograph), a common conventional method to highlight stratigraphic architecture and distri- bution of related units. Mudstones are gray to light brown; sandstones are light gray to white. This process is often performed on photos or a photomosaic acquired in the field.

meander-belt edge

ALBERTA

Figure 2. Traditional geologic map used to share field measurements, observations, and interpretations in 2D plan-view. This geologic map Dinosaur was constructed from the integration of traditional fieldwork methods Provincial (measured sections as well as paleoflow and bedding measurements) Park with digital outcrop model mapping to characterize heterolithic chan- 111.59º W nel-belt deposits exposed at Dinosaur Provincial Park, southeastern Alberta, Canada. Field-based Facies Associations (FA)1—sandy point 50.82º N bar; FA2—heterolithic point bar; FA3—Counter-point bar; FA4—aban- doned channel; FA5—mudstone. Bedding surfaces, noted in Figure 1 Extent of g. 1 (red), were digitally mapped on the 3D model and yield a more refined 3D model Fi and detailed interpretation of accretion surface orientation and stratigraphic architecture. These methods are being widely applied, yet the Measured results are difficult to disseminate and share in 3D. section Strike/Dip of bedding N Interpreted 200 m scroll pattern

FA1 FA2 FA3 FA4 FA5

specialized software, or transfer and storage bottlenecks remain, with a lack of accessible issues relative to underlying base layers of large files. This prompts an increased visualization software and the need to trans- (Tavani et al., 2014). ability to share data sets, interpretations, and fer large files. Web-based dissemination may be one of results with a wider community, expanding Though separate 3D viewers are available the most promising and practical means for opportunities for scientific communication to supplement proprietary software (e.g., rapidly streaming 3D digital data sets with- and open science education. Trimble RealWorks, FugroViewer), they typ- out transferring raw data (Turner, 2006; von ically require local storage of large files, Reumont et al., 2013). Advances of applica- RELATED WORK learning curves, and have associated licens- tion programming interfaces (APIs), such as Visualization of digital 3D models has ing restrictions. Alternative applications, WebGL, allow modern Internet browsers to been practical for more than two decades; such as digital globes (e.g., Google Earth) are access the local GPU to improve rendering of however, early geoscience applications were a popular method for disseminating spatial 2D and 3D graphics, without the need for typically restricted to dedicated geovisual- and non-spatial data in an interactive, semi- plug-ins or extensions (Boutsi et al., 2019). ization labs and required specialized soft- immersive environment, with intuitive con- Though not guaranteed, WebGL enables ware (e.g., Thurmond et al., 2006; Jones et trols (Goodchild et al., 2012). Digital globes GPU functionality on various operating sys- al., 2009; Bilke et al., 2014). Today, visual- have been used to create “virtual field trips” tems and devices (Schuetz, 2016). Several ization of large 3D data sets is no longer lim- (McCaffrey et al., 2010; Simpson and De proprietary web viewers, such as Sketchfab ited to sophisticated labs, but rather an aver- Paor, 2010; De Paor and Whitmeyer, 2011) (https://www.sketchfab.com), use WebGL age computer can render 3D models ef- and present 3D data sets (Blenkinsop, 2012; for sharing 3D models. Proprietary web- ficiently, due in large part to inexpensive De Paor, 2016). Although digital globes pro- based viewers have recently been used by hardware, such as dedicated graphics provide tremendous benefits, displaying DOMs geologic databases (e.g., Safari Database, cessing units (GPUs). Despite the capa- within digital globes requires a significant https://www.safaridb.com: Howell et al., bilities of modern computing hardware, reduction of detail and results in overlay 2014; eRock: Cawood et al., 2019). Web viewers based on open source code, of the park without disrupting wildlife and Web-Based 3D Point Cloud (potree) such as potree (Schuetz, 2016), use WebGL the natural landscape. Viewers using potree code can render raw API to efficiently render massive point point clouds and integrate multiple data sets clouds (>109 points) in standard Internet Data Collection and DOM into a single viewer with customizable browsers. Potree does not require end-users Processing options. The dense point cloud for the 1 km2 to install software or download large data Images were collected through eight field area is ~25.5 GB and contains more sets (Schuetz, 2016) and has been adopted flights with a sensefly eBee fixed-wing UAV than 805 million points (Fig. 3B). Point cloud by various organizations, including the equipped with a Sony WX220 18.2 mega- data sets can be compressed (from .las to .laz USGS, for sharing and visualizing national pixel camera, resulting in 1760 images. format) to reduce file size and converted into topographic LiDAR data sets (USGS, 2019). Images were recorded at a pitch angle of 10º a potree file and folder structure for efficient Similarly, OpenTopography and Pix4D- off-nadir to increase point visibility along tile-based rendering using the potree con- cloud provide online viewers, similar to sub-vertical surfaces and increase precision verter (Schuetz, 2016), with a final size of 3.5 potree, allowing subscribers to share point of final models within the high-relief topog- GB. By default, the potree code includes an clouds through standard web browsers. raphy (Nesbit and Hugenholtz, 2019). Images interactive overview map that displays the Alternative methods have incorporated were processed using Pix4Dmapper v4.3 fol- viewer’s location and view direction, various the use of game engines to create custom- lowing a similar workflow described by pre- navigation options and settings, and several ized geovisualizations compatible with vari- vious authors (Küng et al., 2012; Nesbit et al., measurement tools allowing end-users to ous operating systems. Unity and Unreal 2018). Following initial processing, the record simple measurements, including Engine are two popular game development model was divided into four quadrants and distances, areas, volumes, and topographic platforms that are well-documented, have processed into a dense point cloud and 3D cross sections. Following conversion, the vast online programming communities, and textured mesh. Mesh outputs were exported files and folder structure can be added to a are available for free to developers producing as Autodesk Filmbox (.fbx) format, which web host and dispersed through a standard revenue below a defined threshold. Recently, generally results in smaller file sizes than web domain. Information on getting started game engines have been used in the geosci- commonly used 3D polygon (.ply) and wave- can be found on the potree GitHub page or ences for the gamification and sharing of 3D front (.obj) formats. homepage (http://www.potree.org). An ex- data sets in immersive virtual reality (VR) ample is presented in Figure 3B using the (Bilke et al., 2014), translating ArcGIS data Visualization Approaches Pix4Dcloud viewer, which implements the into a 3D environment using Unity (Robin- DOMs are presented in textured mesh and potree library. son et al., 2015), and presenting virtual dense point cloud formats, using three archaeological sites (Martinez-Rubi et al., different visualization platforms (Sketchfab, Videogame Engine (Unity) 2016; Boutsi et al., 2019). potree, and Unity). Although other platforms Videogame engines allow the production are available, these were intentionally selected of unique end-user experiences through cus- CASE STUDY: FLUVIAL for their ability to provide end-users with tomized data visualization and presentation STRATIGRAPHY, DINOSAUR access to 3D data sets without specialty (Fig. 4). Unity provides a platform to design PROVINCIAL PARK software or transfer of large data sets and are and develop videogames and is well docu- representative of the current capabilities of mented through user manuals, community Geological Overview modern viewers. forums, and online tutorials (e.g., https:// Dinosaur Provincial Park is a UNESCO unity.com/learn/get-started). The program World Heritage Site in southeastern Alberta, Web-Based 3D Mesh (Sketchfab) interface contains simple “drag and drop” Canada, recognized for an abundance of Using a web-based interface, Sketchfab functions for creation of simple scenes, but well-preserved dinosaur fossils and charac- allows authors to intuitively upload models, also allows fully customizable objects and teristic badland topography (Dodson, 1971; define rendering options (e.g., lighting, mate- interaction through scripting. Unity supports Currie and Koppelhus, 2005). This case rial properties), and provide supplementary various formats, including point clouds, study presents a 1 km2 subsection within annotations (Fig. 3A). Upload limitations of meshes, and 2.5D digital elevation models the northeastern portion of the park con- 200 MB, including all mesh and texture com- (DEMs). However, point cloud rendering taining extensive 3D exposures of the ponents, prevented rendering of the complete through Unity can be challenging (Fraiss, Late Cretaceous Dinosaur Park Formation 1 km2 field area within a single viewer without 2017), and DEM interpolations are suscepti- (Wood et al., 1988; Eberth and Hamblin, significant texture distortion. To preserve ble to distortion along slopes (Bellian et al., 1993). Contrasting layers of siltstone and detail within the field area, we present each 2005; Pavlis and Mason, 2017). Therefore, fine- to medium-grained sandstone along quadrant separately. Multiple texture resolu- we used 3D meshes (.fbx files) and associ- with the stratigraphic architecture are rep- tions and VR compatibility are automatically ated textures (.jpg), which made up much of resentative of successive meandering chan- generated during upload to provide end-users the final videogame file size (~1 GB). nel belts cutting through adjacent flood- with different level of detail (LoD) rendering Navigation within the scene was pro- plain mudstones (Figs. 1–2; Smith et al., options based on the capabilities of their view- grammed through a first-person movement 2009; Nesbit et al., 2018; Durkin et al., ing device. Location-specific annotations script, in which the camera is controlled by 2020). Most of the park is a natural preserve describing geologic features and concepts to directional keys on the keyboard and orien- accessible only through research permits or end-users were added to models using the tation based on the mouse. Camera move- guided programs. The digital model pro- upload interface. Additional data sets could ment was restricted within the scene bound- vides a viewing window into a small section not be integrated within 3D model space. aries by enabling the “mesh collider” option A

1 2 Dipping beds

These alternating sandstone and siltstone beds are not at (or horizontal).

They are actually dipping towards the southwest

See #2 for more....

Figure 3. Digital outcrop models (DOMs) of the heterolithic channel-belt deposits in Figure 1, presented in two different viewers. (A) Sketchfab viewer contains 3D textured mesh DOM, but is limited by resolution and only supports text annotations to provide supplemental information; note the limited field area loaded to preserve detail in texture and topography—additional interactive models of the field area are online at https:// sketchfab.com/paulnesbit or by following the QR code. Additional proprietary web viewers include Euclidean Vault (https://www.euclideon.com/ vaultinfo/), and voxxlr (https://www.voxxlr.com/). (B) Visualization of the 3D dense point cloud DOM of the entire 1 km2 field area (>805 million points) in a standard web browser using potree code applied in customized web viewer from Pix4D. QR code provides digital access to the fully interactive viewer, also available at http://tiny.cc/Pix4DpotreeViewer. within the mesh options panel. Various within the user interface (UI) and included viewers; however, a host of challenges remain components were added to the scene, such several “points of interest” that automati- with current solutions before the full potential as the sky background, surrounding topog- cally transport end-users to areas with edu- can be realized. Data acquisition technologies raphy, and interactive features. Sky textures cational information within the scene. The continue to offer higher resolutions and larger were adapted from the Unity Asset Store UI menu allows users to navigate between file sizes. Contrastingly, visualization plat- (assetstore.unity.com). Surrounding topog- integrated data sets and associated informa- forms commonly limit file sizes, forcing a raphy was added by creating a terrain object tion panels within the scene and can be compromise between field area extent and within Unity, defining height values by exited at any time to return to free fly mode. detail. As demand increases for sharing larger importing a 10 m DEM (AltaLIS, 2017), 3D data sets, more advanced multi-resolution textured with a 10-m true-color satellite DISCUSSION rendering solutions, such as LoD in Sketchfab image (Copernicus, 2018). Interactive fea- Sharing of large 3D data sets without spe- and LIME or tiled approaches similar to tures were added to a dropdown menu cialist software is possible through modern potree, will be essential. Options for end- Figure 4. Videogame viewer (executable application) of the entire 1 km2 field area rendered as a textured mesh and created with Unity. Note the dynamic orientation arrow in the upper left corner of the game, the options menu to the right of the screen, and interpretations of geologic surfaces turned “on.” Drop-down menu in the side panel provides end-users with options to navigate to predefined “points of interest” throughout the field area, simulating virtual field-trip stops. Note the resolution difference between the foreground (uninhabited aerial vehicle [UAV]) model and the peripheral topography and landscape, created with a digital elevation model draped with a 10 m satellite image. End-users can also select “free fly” mode in order to navigate throughout the field site on their own. A fully interactive viewer is available in GSA’s Data Repository1 (also accessible from the QR code). Both data repository supplemental files are interactive videogame visualizations presenting a “virtual field trip” that introduces basic geology concepts using a UAV–Structure from Motion textured mesh model within Dinosaur Provincial Park (Alberta, Canada). One is a standalone application (.exe file) for machines running Win- dows (no software required). The other is a standalone application (.app file) for machines running macOS (no software required). Note the README.txt file after unzipping prior to running. users to select display quality based on the render data properly. The default potree code Cartographic principles will become in- capabilities of their machine provides addi- supports basic measurement tools (see Fig. creasingly important as 3D visualizations tional avenues to smoothly render large data 3B), but further customization within potree are used to disseminate spatial data layers sets; for example, the Unity UI offers Quality or Unity requires significant upfront pro- with 3D DOMs. This technique has the and Screen Resolution settings upon startup, gramming efforts. potential to extend models beyond simple and potree code provides adjustable options Compatibility and design considerations visuals into scientific visualizations de- for Point Budget and Quality. may also emerge as issues for visualization signed to aid the understanding of data, Capabilities of 3D viewers can be platforms. Although potree code is cur- provide new perspectives, and provoke expanded through incorporation of basic rently compatible with standard web brows- individual knowledge construction (Mac- interpretation tools, the ability to integrate ers, future updates to browsers may impede Eachren and Kraak, 1997). Delivering data multiple data sets, and customizable inter- performance. Similarly, users who rely on in this way requires consideration of car- faces. There are various levels of customiz- third-party applications are subject to deci- tographic design as it relates to the purpose ability in modern platforms. Sketchfab, for sions made by suppliers. On the other hand, of a model, intended audience, and how to example, currently permits addition of text formats supported by Unity (e.g., Windows best present data. For example, use of these and web-linked photo annotations, but does [.exe], Apple [.app], mobile device [iOS, platforms as geospatial data viewers still not support integration of additional 3D Android], Sony PlayStation 4, Microsoft requires basic map components (e.g., scale, objects, shapefiles, or drawings. Open source Xbox, and WebGL) have been standard for orientation, legend, metadata, etc.), which platforms (e.g., potree and Unity) contain their respective platforms and are likely to are not currently available in some 3D support to integrate meshes, shapefiles, and maintain functionality through updates, as viewers, but are essential for extending custom objects within a scene (Fig. 4) but backward compatibility is often built into these 3D models to spatially meaningful require additional coding to convert and new versions. 3D geovisualizations.

1GSA Data Repository item 2020176, supplemental file 1—virtual field trip videogame for Windows (.exe—no software required); supplemental file 2—virtual field trip videogame for MacOS (.app—no software required), is available online at https://www.geosociety.org/datarepository/2020. CONCLUSIONS AND access to 3D data sets without the need for geoscience education: GSA Today, v. 29, p. 36– RECOMMENDED USE 37, https://doi.org/10.1130/GSATG373GW.1. advanced software and hardware. Though Chesley, J., Leier, A., White, S., and Torres, R., Tools for collecting high-resolution 3D often limited by logistical constraints, we 2017, Using unmanned aerial vehicles and struc- data sets have recently become common- encourage authors to share high-resolution ture-from-motion photogrammetry to character- place in both commercial and academic DOM data sets whenever possible. Methods ize sedimentary outcrops: An example from the fields; however, sharing 3D data sets typi- Morrison Formation, Utah, USA: Sedimentary of 3D data dissemination and visualization Geology, v. 354, p. 1–8, https://doi.org/10.1016/ cally requires end-users to have specialty are still in their infancy behind the relatively j.sedgeo.2017.03.013. software, high-end processing computers, recent rise in 3D mapping applications and CloudCompare, 2019, Version 2.9. GPL Software. and/or locally store large files. Through the acquisition techniques; as the latter continue Available online: http://www.cloudcompare.org presentation of a large UAV-SfM derived to grow, we expect the former to develop in (accessed 7 Feb. 2020). DOM, we introduce three representative Copernicus, 2018, Sentinal data: Retrieved from new and unique ways to facilitate open sci- USGS, Earth Explorer 15 August 2019, pro- visualization platforms that harness poten- ence initiatives through communication and cessed by ESA. tial to advance 3D data dissemination and democratization of photorealistic 3D models. Currie, P.J., and Koppelhus, E.B., editors, 2005, Di- promote open science communication to nosaur Provincial Park: A Spectacular Ancient Ecosystem Revealed: Bloomington, Indiana, In- end-users without the need for specialized ACKNOWLEDGMENTS software and hardware. diana University Press, 648 p. We thank the GSA Today editorial team and two De Paor, D.G., 2016, Virtual rocks: GSA Today, v. 26, Web-based viewers, such as Sketchfab anonymous reviewers for recommendations that p. 4–11, https://doi.org/10.1130/GSATG257A.1. and potree, provide practical options for greatly improved this manuscript, and thanks for re- De Paor, D.G., and Whitmeyer, S.J., 2011, Geologi- sharing data sets with end-users without search permission from Dinosaur Provincial Park cal and geophysical modeling on virtual globes (Research Permit #17-146) and land access from J.G. cumbersome transfer and storage of large using KML, COLLADA, and Javascript: Com- and L.X. files. 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