Vombat: An Open Source Tool for Creating Stratigraphic Logs from Virtual Outcrops
L. Penasa
Center of Studies and Activities for Space, CISAS, “G. Colombo”, University of Padova, Via Venezia 15, 35131 Padova, Italy
Dipartimento di Geoscienze, Via G. Gradenigo, 6, 35131 Padova, Italy
Search for more papers by this authorM. Franceschi
Dipartimento di Geoscienze, Via G. Gradenigo, 6, 35131 Padova, Italy
Search for more papers by this authorN. Preto
Dipartimento di Geoscienze, Via G. Gradenigo, 6, 35131 Padova, Italy
Search for more papers by this authorL. Penasa
Center of Studies and Activities for Space, CISAS, “G. Colombo”, University of Padova, Via Venezia 15, 35131 Padova, Italy
Dipartimento di Geoscienze, Via G. Gradenigo, 6, 35131 Padova, Italy
Search for more papers by this authorM. Franceschi
Dipartimento di Geoscienze, Via G. Gradenigo, 6, 35131 Padova, Italy
Search for more papers by this authorN. Preto
Dipartimento di Geoscienze, Via G. Gradenigo, 6, 35131 Padova, Italy
Search for more papers by this authorAndrea Bistacchi
Department of Environmental and Earth Sciences, University of Milano-Bicocca, Milan, Italy
Search for more papers by this authorMatteo Massironi
Department of Geosciences, University of Padua, Padua, Italy
Search for more papers by this authorSummary
An open source tool, Vombat , is presented that is designed to operate on Virtual Outcrop Models of sedimentary rocks, with the specific aim of assisting the stratigraphic analysis and interpretation. Vombat makes it possible to estimate the average attitude of the bedding and to create one or more attitude-aligned stratigraphic reference frames. This allows Vombat to extract continuous stratigraphic logs of any property associated with the point clouds (e.g. the lidar intensity or RGB color). Stratigraphic logs produced by Vombat can be compared and correlated to typical outcrop logs and petrophysical logs obtained from boreholes (e.g. gamma ray logs) and can provide information about the lithological variations in a stratigraphic succession. Furthermore, Vombat stratigraphic reference frames can be used to associate a stratigraphic position (a depth in the stratigraphic column) to any observation made on the outcrop, allowing visualization in 3D (on the virtual outcrop model) and 1D (on a stratigraphic column) for any collected data. All the geological objects created in the virtual environment can then be saved. The tool has been developed to be user-friendly and is constituted by a dynamically loaded plugin for the open source software CloudCompare.
References
- Bellian , J. , Kerans , C. , and Jennette , D. ( 2005 ). Digital outcrop models: applications of terrestrial scanning lidar technology in stratigraphic .odeling . Journal of Sedimentary Research 75 ( 2 ): 166 – 176 . doi: https://doi.org/10.2110/jsr.2005.013 .
- Bistacchi , A. , Mittempergher , S. , and Martinelli , M. ( 2021 ). Digital outcrop model reconstruction and interpretation . In: 3D Digital Geological Models: From Terrestrial Outcrops to Planetary Surfaces . Wiley, this volume .
- Brodu , N. and Lague , D. ( 2012 ). 3D terrestrial lidar data classification of complex natural scenes using a multi-scale dimensionality criterion: Applications in geomorphology . ISPRS Journal of Photogrammetry and Remote Sensing 68 : 121 – 134 .
- Buckley , S. , Ringdal , K. , Dolva , B. et al. ( 2017 ). LIME: 3D visualisation and interpretation of virtual geoscience models In EGU General Assembly Conference Abstracts . EGU General Assembly Conference Abstracts 19 : 15952 .
- Buckley , S.J. , Enge , H.D. , Carlsson , C. , and Howell , J.A. ( 2010 ). Terrestrial laser scanning for use in virtual outcrop geology . The Photogrammetric Record 25 ( 131 ): 225 – 239 .
- Burton , D. , Dunlap , D.B. , Wood , L.J. , and Flaig , P.P. ( 2011 ). Lidar intensity as a remote sensor of rock properties . Journal of Sedimentary Research 81 ( 5 ): 339 – 347 . doi: https://doi.org/10.2110/jsr.2011.31 .
- Caravaca , G. , Le Mouélic , S. , Mangold , N. et al. ( 2020 ). 3D digital outcrop model reconstruction of the Kimberley outcrop (Gale crater, Mars) and its integration into Virtual Reality for simulated geological analysis . Planetary and Space Science 182 ( 104 ): 808 . doi: https://doi.org/10.1016/j.pss.2019.104808 .
-
Corradetti , A.
,
Seers , T.
,
Billi , A.
, and
Tavani , S.
(
2021
).
Virtual outcrops in a pocket: The Smartphone as a fully equipped photogrammetric data acquisition tool
.
GSA Today
31
(
9
):
4
–
9
. doi:
https://doi.org/10.1130/GSATG506A.1
.
10.1130/GSATG506A.1 Google Scholar
-
Dewez , T.B.
,
Girardeau-Montaut , D.
,
Allanic , C.
, and
Rohmer , J.
(
2016
).
Facets: A Cloudcompare plugin to extract geological planes from unstructured 3D point clouds
.
ISPRS–International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, XLI-B5
799
–
804
. doi: 10.5194/isprsarchives-XLI-B5-799-2016.
10.5194/isprs-archives-XLI-B5-799-2016 Google Scholar
- Dumitriu , T.-C. ( 2013 ). Towards digital preservation of Repedea's big quarry outcrop using “Structure-from-Motion” photogrammetry tools . Analele Stiintifice de Universitatii AI Cuza din Iasi. Sect. 2, Geologie 59 ( 2 ): 19 .
-
Ellis , D.V.
and
Singer , J.M.
(
2007
).
Well Logging for Earth Scientists
,
2nd
e.
Dordrecht, Literaturangaben
:
Springer
.
10.1007/978-1-4020-4602-5 Google Scholar
- Fernández , O. ( 2005 ). Obtaining a best fitting plane through 3D georeferenced data . Journal of Structural Geology 27 ( 5 ): 855 – 858 .
- Franceschi , M. , Teza , G. , Preto , N. et al. ( 2009 ). Discrimination between marls and limestones using intensity data from terrestrial laser scanner . ISPRS Journal of Photogrammetry and Remote Sensing 64 ( 6 ): 522 – 528 . doi: https://doi.org/10.1016/j.isprsjprs.2009.03.003 .
- Franceschi , M. , Preto , N. , Hinnov , L.A. et al. ( 2011 ). Terrestrial laser scanner imaging reveals astronomical forcing in the Early Cretaceous of the Tethys realm . Earth and Planetary Science Letters 305 ( 3–4 ): 359 – 370 . doi: https://doi.org/10.1016/j.epsl.2011.03.017.
- Franceschi , M. , Penasa , L. , Coccioni , R. et al. ( 2015 ). Terrestrial laser scanner imaging for the cyclostratigraphy and astronomical tuning of the Ypresian–Lutetian pelagic section of Smirra (Umbria–Marche Basin, Italy).). Palaeogeography, Palaeoclimatology, Palaeoecology 440 : 33 – 46 . doi: https://doi.org/10.1016/j.palaeo.2015.08.027 .
- Girardeau-Montaut , D. ( 2014 ). Cloudcompare, a 3D point cloud and mesh processing free software . Telecom Paris Tech : EDF R&D .
- Hartzell , P. , Glennie , C. , Biber , K. , and Khan , S. ( 2014 ). Application of multispectral LiDAR to automated virtual outcrop geology . ISPRS Journal of Photogrammetry and Remote Sensing 88 : 147 – 155 . doi: https://doi.org/10.1016/j.isprsjprs.2013.12.004 .
-
Hastie , T.
,
Tibshirani , R.
, and
Friedman , J.
(
2009
).
The Elements of Statistical Learning
,
2nd
e, vol.
1
.
New York
:
Springer Series in Statistics
.
10.1007/978-0-387-84858-7 Google Scholar
- Hinnov , L.A. ( 2013 ). Cyclostratigraphy and its revolutionizing applications in the earth and planetary sciences . Geological Society of America Bulletin 125 ( 11–12 ): 1703 – 1734 . doi: https://doi.org/10.1130/B30934.1 .
- Krupnik , D. , Khan , S. , Okyay , U. et al. ( 2016 ). Study of Upper Albian rudist buildups in the Edwards Formation using ground-based hyperspectral imaging and terrestrial laser scanning . Sedimentary Geology 345 : 154 – 167 . doi: https://doi.org/10.1016/j.sedgeo.2016.09.008 .
- Kurz , T.H. , Buckley , S.J. , Howell , J.A. , and Schneider , D. ( 2008 ). Geological outcrop modelling and interpretation using ground based hyperspectral and laser scanning data fusion . International Archives of Photogrammetry, Remote Sensing and Spatial Information Sciences 37 : B5 .
- Kurz , T.H. , Dewit , J. , Buckley , S.J. et al. ( 2012a ). Hyperspectral image analysis of different carbonate lithologies (limestone, karst and hydrothermal dolomites): The Pozalagua Quarry case study (Cantabria, North-West Spain): Hyperspectral image analysis of carbonate lithologies . Sedimentology 59 ( 2 ): 623 – 645 . doi: https://doi.org/10.1111/j.1365-3091.2011.01269.x .
- Kurz , T.H. , Buckley , S.J. , and Howell , J.A. ( 2012b ). Close range hyperspectral imaging integrated with terrestrial LiDAR scanning applied to rock characterization at centimeter scale. International Arch . Photogramm. Remote Sens. Spat. Inf. Science 34 : 417 – 422 .
- Lague , D. , Brodu , N. , and Leroux , L. ( 2013 ). Accurate 3D comparison of complex topography with terrestrial laser scanner: Application to the Rangitikei canyon (N-Z) . ISPRS Journal of Photogrammetry and Remote Sensing 82 : 10 – 26 . doi: https://doi.org/10.1016/j.isprsjprs.2013.04.009 .
- Lozar , F. , Clari , P. , Dela Pierre , F. et al. ( 2015 ). Virtual tour of past environmental and climate change: The Messinian Succession of the Tertiary Piedmont Basin (Italy) . Geoheritage 7 ( 1 ): 47 – 56 . doi: https://doi.org/10.1007/s12371-014-0098-8 .
- Malkamäki , T. , Kaasalainen , S. , and Ilinca , J. ( 2019 ). Portable hyperspectral lidar utilizing 5 GHz multichannel full waveform digitization . Optics Express 27 ( 8 ): A468 – A480 . doi: https://doi.org/10.1364/OE.27.00A468 .
- Marques , A. , Horota , R.K. , de Souza , E.M. et al. ( 2020 ). Virtual and digital outcrops in the petroleum industry: A systematic review . Earth-Science Reviews 208 ( 103 ): 260 . doi: https://doi.org/10.1016/j.earscirev.2020.103260 .
-
Martinsen , O.J.
,
Pulham , A.J.
,
Haughton , P.D.
, and
Sullivan , M.D.
(
2011
).
Outcrops Revitalized: Tools
.
SEPM
:
Techniques and Applications
.
10.2110/sepmcsp.10 Google Scholar
- Miall , A.D. ( 2016 ). The Stratigraphic-Sedimentologic Data Base , 33 – 75 . Cham : Springer International Publishing doi: https://doi.org/10.1007/978-3-319-24304-7_2 .
- Mountrakis , G. , Im , J. , and Ogole , C. ( 2011 ). Support vector machines in remote sensing: A review . ISPRS Journal of Photogrammetry and Remote Sensing 66 ( 3 ): 247 – 259 . doi: https://doi.org/10.1016/j.isprsjprs.2010.11.001 .
- Penasa , L. , M. Franceschi , M. , Preto , N. et al. ( 2014 ). Integration of intensity textures and local geometry descriptors from Terrestrial Laser Scanning to map chert in outcrops . ISPRS Journal of Photogrammetry and Remote Sensing 93 : 88 – 97 . doi: https://doi.org/10.1016/j.isprsjprs.2014.04.003 .
- Penasa , L. , Franceschi , M. , Gattolin , G. et al. ( 2019 ). Cyclostratigraphic investigations in the Calcare Massiccio (Early Jurassic, Umbria-Marche Basin) through photogrammetry . In: 250 Million Years of Earth History in Central Italy: Celebrating 25 Years of the Geological Observatory of Coldigioco, Geological Society of America Special Paper , vol. 542 , 87 – 103 .
-
Rarity , F.
,
van Lanen , X.M.T.
,
Hodgetts , D.
et al. (
2014
).
LiDAR-based digital outcrops for sedimentological analysis: Workflows and techniques
.
Geological Society, London, Special Publications
387
(
1
):
153
–
183
. doi:
https://doi.org/10.1144/SP387.5
.
10.1144/SP387.5 Google Scholar
-
A. Salvador
(ed.) (
2013
).
International Stratigraphic Guide: A Guide to Stratigraphic Classification, Terminology, and Procedure
.
Boulder, Colorado
:
Geological Society of America
doi: 10.1130/9780813774022.
10.1130/9780813774022 Google Scholar
- Shakarji , C.M. and Srinivasan , V. ( 2013 ). Theory and algorithms for weighted total least-squares fitting of lines, planes, and parallel planes to support tolerancing standards . Journal of Computing and Information Science in Engineering 13 ( 3 ): 031,008 .
-
Sterzai , P.
,
Vellico , M.
,
Berti , M.
et al. (
2010
).
LiDAR and hyperspectral data integration for landslide monitoring: The test case of Valoria landslide
.
Italian Journal of Remote Sensing
42
(
3
):
89
–
99
.
10.5721/ItJRS20104237 Google Scholar
- Summerfield , M. ( 2011 ). Advanced QT Programming: Creating Great Software with C++ and QT 4 . Upper Saddle River, NJ : Prentice-Hall .
- Suomalainen , J. , Hakala , T. , Kaartinen , H. et al. ( 2011 ). Demonstration of a virtual active hyperspectral LiDAR in automated point cloud classification . ISPRS Journal of Photogrammetry and Remote Sensing 66 ( 5 ): 637 – 641 . doi: https://doi.org/10.1016/j.isprsjprs.2011.04.002 .
- Tavani , S. , Arbues , P. , Snidero , M. et al. ( 2011 ). Open Plot Project: An open-source toolkit for 3-D structural data analysis . Solid Earth 2 ( 1 ): 53 – 63 . doi: https://doi.org/10.5194/se-2-53-2011 .
- Telling , J. , Lyda , A. , Hartzell , P. , and Glennie , C. ( 2017 ). Review of Earth science research using terrestrial laser scanning . Earth-Science Reviews 169 : 35 – 68 . doi: https://doi.org/10.1016/j.earscirev.2017.04.007 .
- Thiele , S.T. , Grose , L. , Samsu , A. et al. ( 2017 ). Rapid, semi-automatic fracture and contact mapping for point clouds, images and geophysical data . Solid Earth 8 ( 6 ): 1241 – 1253 . doi: https://doi.org/10.5194/se-8-1241-2017 .
- Thiele , S.T. , Lorenz , S. , Kirsch , M. et al. ( 2021 ). Multi-scale, multi-sensor data integration for automated 3-D geological mapping . Ore Geology Reviews 136 ( 104 ): 252 . doi: https://doi.org/10.1016/j.oregeorev.2021.104252 .
- Wilkinson , M. , Jones , R. , Woods , C. et al. ( 2016 ). A comparison of terrestrial laser scanning and structure-from-motion photogrammetry as methods for digital outcrop acquisition . Geosphere 12 ( 6 ): 1865 – 1880 . doi: https://doi.org/10.1130/GES01342.1 .
- Woodcock , N.H. ( 1977 ). Specification of fabric shapes using an eigenvalue method . Geological Society of America Bulletin 88 ( 9 ): 1231 – 1236 .