Uso de nubes de puntos 3D para identificación y caracterización de familias de discontinuidades planas en afloramientos rocosos y evaluación de la calidad geomecánica

En este trabajo se estudia el uso de las nubes de puntos en 3D, es decir, un conjunto de puntos en un sistema de referencia cartesiano en R3, para la identificación y caracterización de las discontinuidades que afloran en un macizo rocoso y su aplicación al campo de la Mecánica de Rocas. Las nubes de puntos utilizadas se han adquirido mediante tres técnicas: sintéticas, 3D laser scanner y la técnica de fotogrametría digital Structure From Motion (SfM). El enfoque está orientado a la extracción y caracterización de familias de discontinuidades y su aplicación a la evaluación de la calidad de un talud rocoso mediante la clasificación geomecánica Slope Mass Rating (SMR). El contenido de la misma está dividido en tres bloques, como son: (1) metodología de extracción de discontinuidades y clasificación de la nube de puntos 3D; (2) análisis de espaciados normales en nubes de puntos 3D; y (3) análisis de la evaluación de la calidad geomecánica de taludes rocoso mediante la clasificación geomecánica SMR a partir de nubes de puntos 3D. La primera línea de investigación consiste en el estudio de las nubes de puntos 3D con la finalidad de extraer y caracterizar las discontinuidades planas presentes en la superficie de un macizo rocoso. En primer lugar, se ha recopilado información de las metodologías existentes y la disponibilidad de programas para su estudio. Esto motivó la decisión de investigar y diseñar un proceso de clasificación novedoso, que muestre todos los pasos para su programación e incluso ofreciendo el código programado a la comunidad científica bajo licencia GNU GPL. De esta forma, se ha diseñado una novedosa metodología y se ha programado un software que analiza nubes de puntos 3D de forma semi-automática, permitiendo al usuario interactuar con el proceso de clasificación. Dicho software se llama Discontinuity Set Extractor (DSE). El método se ha validado empleando nubes de puntos sintéticas y adquiridas con 3D laser scanner. En primer lugar, este código analiza la nube de puntos efectuando un test de coplanaridad para cada punto y sus vecinos próximos para, a continuación, calcular el vector normal de la superficie en el punto estudiado. En segundo lugar, se representan los polos de los vectores normales calculados en el paso previo en una falsilla estereográfica. A continuación se calcula la densidad de los polos y los polos con mayor densidad o polos principales. Estos indican las orientaciones de la superficie más representadas, y por tanto las familias de discontinuidades. En tercer lugar, se asigna a cada punto una familia en dependencia del ángulo formado por el vector normal del punto y el de la familia. En este punto el usuario puede visualizar la nube de puntos clasificada con las familias de discontinuidades que ha determinado para validar el resultado intermedio. En cuarto lugar, se realiza un análisis cluster en el que se determina la agrupación de puntos según planos para cada familia (clusters). A continuación, se filtran aquellos que no tengan un número de puntos suficiente y se determina la ecuación de cada plano. Finalmente, se exportan los resultados de la clasificación a un archivo de texto para su análisis y representación en otros programas. La segunda línea de investigación consiste en el estudio del espaciado entre discontinuidades planas que afloran en macizos rocosos a partir de nubes de puntos 3D. Se desarrolló una metodología de cálculo de espaciados a partir de nubes de puntos 3D previamente clasificadas con el fin de determinar las relaciones espaciales entre planos de cada familia y calcular el espaciado normal. El fundamento novedoso del método propuesto es determinar el espaciado normal de familia basándonos en los mismos principios que en campo, pero sin la restricción de las limitaciones espaciales, condiciones de inseguridad y dificultades inherentes al proceso. Se consideraron dos aspectos de las discontinuidades: su persistencia finita o infinita, siendo la primera el aspecto más novedoso de esta publicación. El desarrollo y aplicación del método a varios casos de estudio permitió determinar su ámbito de aplicación. La validación se llevó a cabo con nubes de puntos sintéticas y adquiridas con 3D laser scanner. La tercera línea de investigación consiste en el análisis de la aplicación de la información obtenida con nubes de puntos 3D a la evaluación de la calidad de un talud rocoso mediante la clasificación geomecánica SMR. El análisis se centró en la influencia del uso de orientaciones determinadas con distintas fuentes de información (datos de campo y técnicas de adquisición remota) en la determinación de los factores de ajuste y al valor del índice SMR. Los resultados de este análisis muestran que el uso de fuentes de información y técnicas ampliamente aceptadas pueden ocasionar cambios en la evaluación de la calidad del talud rocoso de hasta una clase geomecánica (es decir, 20 unidades). Asimismo, los análisis realizados han permitido constatar la validez del índice SMR para cartografiar zonas inestables de un talud. Los métodos y programas informáticos desarrollados suponen un importante avance científico para el uso de nubes de puntos 3D para: (1) el estudio y caracterización de las discontinuidades de los macizos rocosos y (2) su aplicación a la evaluación de la calidad de taludes en roca mediante las clasificaciones geomecánicas. Asimismo, las conclusiones obtenidas y los medios y métodos empleados en esta tesis doctoral podrán ser contrastadas y utilizados por otros investigadores, al estar disponibles en la web del autor bajo licencia GNU GPL.

Using Terrestrial LiDAR to Monitor Erosion within the Gold Basin Landslide Complex, Verlot, WA

In 2014 the United States Forest Service closed the Gold Basin Campground of western Washington in an effort to protect the public from unstable hillslopes directly adjacent to the campground. The Gold Basin Landslide Complex (GBLC) is actively eroding via block fall, dry ravel, and debris flows, which contribute sediment into the South Fork of the Stillaguamish River. This sediment diminishes the salmonid population within the South Fork of the Stillaguamish River by reducing habitable spawning grounds, which is a big concern to the Stillaguamish Tribe of Indians. In this investigation, I quantified patterns of degradation and total volume of sediment erosion from the middle lobe of the GBLC over the period of July 2015 through January 2016 using terrestrial (ground-based) LiDAR (TLS). I characterized site specific stratigraphy and geomorphic processes, and laid the groundwork for future, long-term monitoring of this site. Results of this investigation determined that ~ 4,800m3 of sediment was eroded from the middle lobe of the GBLC during the 6 month study period (July 2015 – January 2016). This erosion likely occurred from debris flows, raveling of poorly sorted sand and gravel deposits and block failures of high plasticity silts and clays, and/or other mass wasting mechanisms. The generalized stratigraphic sequence in the GBLC consists of alternating massive beds of sand and gravel with silts and clays. The low permeability of these silts and clays provide a perfect venue for groundwater to percolate, as I observed during field investigations, which likely contributes to the active instability of the hillslopes. Continued monitoring and mapping of this complex will lead to viable information that could help both the United States Forest Service and the Stillaguamish Tribe.

Observations of Joints Present in the Lawton Clay Member of the Vashon Stade, Exposed at a Coastal Bluff in Discovery Park, Seattle, Washington

The southwest-facing coastal bluff present at Discovery Park, Seattle, Washington, displays distinctive joints throughout the exposed Lawton Clay Member. Exhibiting a characteristic local stratigraphy of permeable advance outwash over the impermeable proglacial lacustrine clay, this bluff is located in an area of Seattle at high risk from landslides. This project addressed the relationship between the joints observed at this coastal bluff and the coherency of the bluff as a whole, through remote sensing and field measurements. Aerial drone photography taken of the bluff was processed through a photogrammetry software to produce a 3-dimensional Structure from Motion model, allowing for a digital manipulation and broad examination of the bluff not possible by foot. Stereonet plots produced from these measurements provided insight into patterns of varying joint strike along a horizontal transect of the observed bluff face. Taken together, these two visualizations provided a better picture of the possible chicken-and-egg interaction of the joints and bluff topography; they demonstrated the likelihood that the joint formation at the bluff was most likely to be primarily influenced by the local topography of the bluff over other sources of possible tensional stress in the immediate area.

Modelo para reconstrução 3D de cenas baseado em imagens

3D Reconstruction is the process used to obtain a detailed graphical model in three dimensions that represents some real objectified scene. This process uses sequences of images taken from the scene, so it can automatically extract the information about the depth of feature points. These points are then highlighted using some computational technique on the images that compose the used dataset. Using SURF feature points this work propose a model for obtaining depth information of feature points detected by the system. At the ending, the proposed system extract three important information from the images dataset: the 3D position for feature points; relative rotation and translation matrices between images; the realtion between the baseline for adjacent images and the 3D point accuracy error found.

Rilievo fotogrammetrico da drone per la generazione di modelli termici di porzioni di territorio

In questo elaborato viene sperimentato un iter processuale che consenta di utilizzare i sensori termici affiancati a fotocamere digitale in ambito fotogrammetrico al fine di ottenere prodotto dal quale sono estrapolabili informazioni geometriche e termiche dell’oggetto di studio. Il rilievo fotogrammetrico è stato svolto mediante l’utilizzo di un drone con equipaggiamento multisensoriale, termico e digitale, su una porzione di territorio soggetto ad anomalie termiche nei pressi di Medolla (MO). Per l’analisi termica e geometrica sono stati posizionati sul campo 5 target termici di cui ne sono state misurate le coordinate per la georeferenziazione delle nuvole dense di punti e la temperatura. In particolare sono state eseguite due riprese aeree dalle quali sono stati estratti i frame necessari per i processi di restituzione fotogrammetrica. Le immagini sono state sottoposte ad una fase di trattamento che ha prodotto immagini rettificate prive di delle distorsioni impresse dall’obbiettivo. Per la creazione degli elaborati vettoriali e raster a colori e termici sono stati impiegati inizialmente software di fotogrammetria digitale in grado di fornire scene tridimensionali georeferenziate dell’oggetto. Sono state sviluppate sia in un ambiente open-source, sia sfruttando programmi commerciali. Le nuvole dense sono state successivamente trattate su una piattaforma gratuita ad interfaccia grafica. In questo modo è stato possibile effettuare dei confronti tra i diversi prodotti e valutare le potenzialità dei software stessi. Viene mostrato come creare un modello tridimensionale, contenente sia informazioni geometriche che informazioni termiche, partendo dalla nuvola termica e da quella a colori. Entrambe georeferenziate utilizzando gli stessi punti fotogrammetrici d’appoggio. Infine i prodotti ottenuti sono stati analizzati in un ambiente GIS realizzando sovrapposizioni grafiche, confronti numerici, interpolazioni, sezioni e profili.

Photographs of the Mount Meager, southwestern British Columbia

On August 6, 2010, a large (~50 Mm**3) debris avalanche occurred on the flank of Mount Meager in the southern Coast Mountains of British Columbia, Canada. We studied the deposits to infer the morphodynamics of the landslide from initiation to emplacement. Structure from motion (SfM) photogrammetry, based on oblique photos taken with a standard SLR camera during a low helicopter traverse, was used to create high-resolution orthophotos and base maps. Interpretation of the images and maps allowed us to recognize two main rheological phases in the debris avalanche. Just below the source area, in the valley of Capricorn Creek, the landslide separated into two phases, one water-rich and more mobile, and the other water-poor and less mobile. The water-rich phase spread quickly, achieved high superelevation on the valley sides, and left distal scattered deposits. The main water-poor phase moved more slowly, did not superelevate, and formed a thick continuous deposit (up to ~30 m) on the valley floor. The water-poor flow deposit has structural features such as hummocks, brittle-ductile faults, and shear zones. Our study, based on a freshly emplaced deposit, advances understanding of large mass movements by showing that a single landslide can develop multiple rheology phases with different behaviours. Rheological evolution and separation of phases should always be taken into account to provide better risk assessment scenarios.

La generazione di modelli tridimensionali densi in ambito architettonico mediante la fotogrammetria digitale

The Italian territory offers a wide range of treasures in the field of Cultural Assets. This is a highly relevant property, which needs an accurate management and preservation performed by appropriate tools, also giving attention to the maintenance and safeguard from risk factors. Nowadays the increasing development of new digital technologies, added by remarkable steps forward got by the subject of Geomatic makes possible an efficient integration among different techniques, helped also by spread of solutions to improve the data import-export and transmission between different devices. The main objective of this thesis is to experience the photogrammetric restitution implemented in a commercial software of digital photogrammetry, in order to generate a dense 3D model of the facade of the Basilica Sant'Apollinare Nuovo in Ravenna. The 1st Chapter, after a general introduction regarding the 3D survey of Cultural Heritage and some considerations linked to the use of digital photogrammetry in this field, is focused to analyze the case of stereoscopic and the monoscopic approach. In particular, it develops the theme of close-range photogrammetry. The 2nd Chapter, exposes the theme of digital images, from color theory until their appearing on the monitor. The 3rd Chapter, develops the case study of the Basilica di Sant'Apollinare Nuovo, the historical, architectural and religious of the same. Also, it is examined the issue of photogrammetry and laser scanning of the case study. The final part of the same chapter, treats the processing of data processing the software Agisoft PhotoScan, in order to generate, by means of Structure from Motion technique, a digital geometric 3D model of the Basilica Facade. The digital model has been scaled on the basis of measurements made on the field. With the software it was possible to accomplish the three phases of the photogrammetric data processing: internal orientation, exterior orientation and restitution.

Exploring the World's Visual History

Thesis (Ph.D.)--University of Washington, 2016-08

Improving the Accuracy of 3-D Reconstruction in Robotic Vision Applications

Thesis (Ph.D.)--University of Washington, 2016-08

POSE ESTIMATION AND 3D RECONSTRUCTION USING SENSOR FUSION

A camera maps 3-dimensional (3D) world space to a 2-dimensional (2D) image space. In the process it loses the depth information, i.e., the distance from the camera focal point to the imaged objects. It is impossible to recover this information from a single image. However, by using two or more images from different viewing angles this information can be recovered, which in turn can be used to obtain the pose (position and orientation) of the camera. Using this pose, a 3D reconstruction of imaged objects in the world can be computed. Numerous algorithms have been proposed and implemented to solve the above problem; these algorithms are commonly called Structure from Motion (SfM). State-of-the-art SfM techniques have been shown to give promising results. However, unlike a Global Positioning System (GPS) or an Inertial Measurement Unit (IMU) which directly give the position and orientation respectively, the camera system estimates it after implementing SfM as mentioned above. This makes the pose obtained from a camera highly sensitive to the images captured and other effects, such as low lighting conditions, poor focus or improper viewing angles. In some applications, for example, an Unmanned Aerial Vehicle (UAV) inspecting a bridge or a robot mapping an environment using Simultaneous Localization and Mapping (SLAM), it is often difficult to capture images with ideal conditions. This report examines the use of SfM methods in such applications and the role of combining multiple sensors, viz., sensor fusion, to achieve more accurate and usable position and reconstruction information. This project investigates the role of sensor fusion in accurately estimating the pose of a camera for the application of 3D reconstruction of a scene. The first set of experiments is conducted in a motion capture room. These results are assumed as ground truth in order to evaluate the strengths and weaknesses of each sensor and to map their coordinate systems. Then a number of scenarios are targeted where SfM fails. The pose estimates obtained from SfM are replaced by those obtained from other sensors and the 3D reconstruction is completed. Quantitative and qualitative comparisons are made between the 3D reconstruction obtained by using only a camera versus that obtained by using the camera along with a LIDAR and/or an IMU. Additionally, the project also works towards the performance issue faced while handling large data sets of high-resolution images by implementing the system on the Superior high performance computing cluster at Michigan Technological University.

Assessing the relationship between bee/flower diversity and vegetation structural heterogeneity through UAV photogrammetry

The ecosystem services provided by bees are very important. Factors as habitat fragmentation, intensive agriculture and climate change are contributing to the decline of bee populations. The use of remote sensing could be a useful tool for the recognition of sites with a high diversity, before performing a more expensive survey in the field. In this study the ability of Unmanned Aerial Vehicles (UAV) images to estimate biodiversity at local scale has been analysed testing the concept of the Height Variation Hypothesis (HVH). This approach states that, the higher the vegetation height heterogeneity (HH) measured by remote sensing information, the higher the vertical complexity and the higher vegetation species diversity. In this thesis the concept has been brought to a higher level, in order to understand if the vegetation HH can be considered a proxy also of bee species diversity and abundance. We tested this approach collecting field data on bees/flowers and RGB images through an UAV campaign in 30 grasslands in the South of the Netherlands. The Canopy Height Model (CHM) were derived through the photogrammetry technique "Structure from Motion" (SfM) with resolutions of 10cm, 25cm, 50cm. Successively, the HH assessed on the CHM using the Rao's Q heterogeneity index was correlated to the field data (bee abundance, diversity and bee/flower species richness). The correlations were all positive and significant. The highest R2 values were found when the HH was calculated at 10cm and correlated to bee species richness (R2 = 0.41) and Shannon’s H index (R2 = 0.38). Using a lower spatial resolution the goodness of fit slightly decreases. For flower species richness the R2 ranged between 0.36 to 0.39. Our results suggest that methods based on the concept behind the HVH, in this case deriving information of HH from UAV data, can be developed into valuable tools for large-scale, standardized and cost-effective monitoring of flower diversity and of the habitat quality for bees.

pido, a non-long terminal repeat retrotransposon of the chicken repeat 1 family from the genome of the Oriental blood fluke, Schistosoma japonicum

A newly described non-long terminal repeat (non-LTR) retrotransposon element was isolated from the genome of the Oriental schistosome, Schistosoma japonicum. At least 1000 partial copies of the element, which was named pido, were dispersed throughout the genome of S. japonicum. As is usual with non-LTR retrotransposons, it is expected that many pido elements will be 5'-truncated. A consensus sequence of 3564 bp of the truncated pido element was assembled from several genomic fragments that contained pido-hybridizing sequences. The sequence encoded part of the first open reading frame (ORF), the entire second ORF and, at its 3'-terminus, a tandemly repetitive, A-rich (TA(6)TA(5)TA(8)) tail, The ORF1 of pido encoded a nucleic acid binding protein and ORF2 encoded a retroviral-like polyprotein that included apurinic/apyrimidinic endonuclease (EN) and reverse transcriptase (RT) domains, in that order. Based on its sequence and structure, and phylogenetic analyses of both the RT and EN domains, pido belongs to the chicken repeat 1 (CR1)-like lineage of elements known from the chicken, turtle, puffer fish, mosquitoes and other taxa. pido shared equal similarity with CRI from chicken, an uncharacterized retrotransposon from Caenorhabditis elegans and SR1 (a non-LTR retrotransposon) from the related blood fluke Schistosoma mansoni; the level of similarity between pido and SR1 indicated that these two schistosome retrotransposons were related but not orthologous. The findings indicate that schistosomes have been colonized by at least two discrete CRI-like elements. Whereas pido did not appear to have a tight target site specificity, at least one copy of pido has inserted into the 3'-untranslated region of a protein-encoding gene (GeriBank AW736757) of as yet unknown identity. mRNA encoding the RT of pido was detected by reverse transcription-polymerase chain reaction in the egg, miracidium. and adult developmental stages of S. japonicum, indicating that the RT domain was transcribed and suggesting that pido was replicating actively and mobile within the S. japonicum genome. (C) 2002 Elsevier Science B.V. All rights reserved.

Wall motion estimation in intracranial aneurysms

The quantification of wall motion in cerebral aneurysms is becoming important owing to its potential connection to rupture, and as a way to incorporate the effects of vascular compliance in computational fluid dynamics (CFD) simulations.Most of papers report values obtained with experimental phantoms, simulated images, or animal models, but the information for real patients is limited. In this paper, we have combined non-rigid registration (IR) with signal processing techniques to measure pulsation in real patients from high frame rate digital subtraction angiography (DSA). We have obtained physiological meaningful waveforms with amplitudes in therange 0mm-0.3mm for a population of 18 patients including ruptured and unruptured aneurysms. Statistically significant differences in pulsation were found according to the rupture status, in agreement with differences in biomechanical properties reported in the literature.

Cardiac motion estimation by joint alignment of tagged MRI sequences

Image registration has been proposed as an automatic method for recovering cardiac displacement fields from Tagged Magnetic Resonance Imaging (tMRI) sequences. Initially performed as a set of pairwise registrations, these techniques have evolved to the use of 3D+t deformation models, requiring metrics of joint image alignment (JA). However, only linear combinations of cost functions defined with respect to the first frame have been used. In this paper, we have applied k-Nearest Neighbors Graphs (kNNG) estimators of the -entropy (H ) to measure the joint similarity between frames, and to combine the information provided by different cardiac views in an unified metric. Experiments performed on six subjects showed a significantly higher accuracy (p < 0.05) with respect to a standard pairwise alignment (PA) approach in terms of mean positional error and variance with respect to manually placed landmarks. The developed method was used to study strains in patients with myocardial infarction, showing a consistency between strain, infarction location, and coronary occlusion. This paper also presentsan interesting clinical application of graph-based metric estimators, showing their value for solving practical problems found in medical imaging.

Nonrigid Motion Compensation of Free Breathing Acquired Myocardial Perfusion Data

In this work, we present a novel method to compensate the movement in images acquired during free breathing using first-pass gadolinium enhanced, myocardial perfusion magnetic resonance imaging (MRI). First, we use independent component analysis (ICA) to identify the optimal number of independent components (ICs) that separate the breathing motion from the intensity change induced by the contrast agent. Then, synthetic images are created by recombining the ICs, but other then in previously published work (Milles et al. 2008), we omit the component related to motion, and therefore, the resulting reference image series is free of motion. Motion compensation is then achieved by using a multi-pass non-rigid image registration scheme. We tested our method on 15 distinct image series (5 patients) consisting of 58 images each and we validated our method by comparing manually tracked intensity profiles of the myocardial sections to automatically generated ones before and after registration. The average correlation to the manually obtained curves before registration 0:89 0:11 was increased to 0:98 0:02