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No. of bitstreams: 1 oliveira_ra_dr_prud.pdf: 10400710 bytes, checksum: 4c4e6b235bd849c0d16074edea702847 (MD5) Previous issue date: 2017-06-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Recentemente, os sensores hiperespectrais miniaturizados entraram no mercado e alguns modelos adquirem bandas hiperespectrais com geometria de quadro, com a vantagem de serem também operados em veículos aéreos remotamente pilotados (VARP). As imagens deste tipo de câmara podem ser utilizadas para a geração de modelos digitais de superfície hiperespectral (MDSHs) de alta resolução, usando o VARP, sem a necessidade do registro de dados de diferentes sensores ou diferente datas de aquisição. MDSHs aumentam o conhecimento sobre os alvos, uma vez que permitem modelar a reflectância do alvo utilizando dados provenientes de diferentes direções. Neste trabalho, a câmara hiperespectral de quadro utilizada não adquire todas as bandas instantaneamente, causando um deslocamento entre as bandas devido ao movimento da plataforma. Os principais objetivos deste projeto foram estudar e desenvolver técnicas para a geração de MDSHs em áreas de florestas, investigando e avaliando as principais etapas para o processamento das imagens da câmara hiperespectral de quadro até a geração do MSDH. Considerando que a tecnologia da câmara baseia-se em filtros ajustáveis, o estudo avaliou: a auto-calibração da câmara, verificando o comportamento dos parâmetros de orientação interior em diferentes bandas espectrais; o corregistro das bandas através de transformações geométricas 2D; e a estimativa dos parâmetros de orientação exterior. Em relação à geração do MDS, uma abordagem baseada em correspondência de imagem no espaço do objeto foi desenvolvida, adaptando o método de busca em linha vertical (VLL) para a geração MDSH e foi nomeado como VLL hiperespectral (HVLL). Adicionalmente, o uso de imagens classificadas para a adaptação dos parâmetros de correspondência foi avaliado com o objetivo de melhorar o processo de correspondência para diferentes objetos (HVLLC). Posteriormente, foram utilizadas múltiplas bandas no processo de correspondência de imagens, dados como múltiplos ângulos de visada e informação espectral foram calculados simultaneamente ao processo de correspondência de imagens. A avaliação da qualidade foi realizada comparando-se os MDSs gerados com os produzidos por um software comercial e por dados Airborne Laser Scanning (ALS). Esta investigação demonstrou que a técnica proposta pode ser usada para a geração de modelos 3D integrados aos dados hiperespectrais multiangulares da câmara hiperespectral de quadro. A avaliação de todas as etapas demonstrou que esta tecnologia pode fornecer dados geométricos e espectrais precisos e os MDSHs resultantes possuem potencial para várias aplicações de sensoriamento remoto. / Recently, miniaturized hyperspectral sensors, operable from small Remotely Piloted Aerial Systems (RPAS), have entered the market and some of these sensors acquire hyperspectral bands in frame geometry. Images of the lightweight hyperspectral 2D frame camera can be used to generate high-resolution hyperspectral digital surface models (HDSMs), without the registration of data from different sensors or different dates of acquisition. HSDMs increase the knowledge about the targets since it allows modeling the target reflectance using data coming from different directions. In this study, the hyperspectral 2D frame camera used does not acquire all bands instantaneously, causing band misalignment due to the platform motion. The main aims of this project were to study and develop techniques for the generation of HDSMs in forest areas, studying and assessing the main steps to process the hyperspectral 2D frame camera images until the HDSM generation. Considering that the camera technology is based on tunable filters, the study have assessed the orientation and DSM generation steps: the self-calibrating bundle adjustment to verify the behaviour of the interior orientation parameters using different spectral bands; the co-registration of the bands using 2D geometric transformation; the exterior orientation parameter estimation. Regarding to the DSM generation, an approach based on object space image matching was developed, adapting the vertical line locus (VLL) method for HDSM generation, and was named as hyperspectral VLL (HVLL). Additionally, the use of image classification data was investigated in order to adapt the image matching parameters and improve the process of image matching for different objects (hyperspectral VLL classes - HVLLC). Further, multiple bands were used and the spectral and multiangular viewing geometry were computed simultaneously to the image matching method. Quality assessment was performed by comparing to DSMs generated to those produced by commercial software and also by Airborne Laser Scanning (ALS) data. This investigation demonstrated that the proposed technique can be used to generate integrated 3D information and multiangular hyperspectral data from hyperspectral 2D frame camera. The assessment of all steps showed that the hyperspectral 2D frame technology can provide accurate geometric and spectral data and the resulting HDSMs have potential for several remote sensing applications. / FAPESP: 2013/17787-3 / FAPESP: 2013/14444-0 / FAPESP: 2014/24844-6

Ces travaux se placent dans le contexte de l'étude des champs profonds hyperspectraux produits par l'instrument d'observation céleste MUSE. Ces données permettent de sonder l'Univers lointain et d'étudier les propriétés physiques et chimiques des premières structures galactiques et extra-galactiques. La première problématique abordée dans cette thèse est l'attribution d'une signature spectrale pour chaque source galactique. MUSE étant un instrument au sol, la turbulence atmosphérique dégrade fortement le pouvoir de résolution spatiale de l'instrument, ce qui génère des situations de mélange spectral pour un grand nombre de sources. Pour lever cette limitation, des approches de fusion de données, s'appuyant sur les données complémentaires du télescope spatial Hubble et d'un modèle de mélange linéaire, sont proposées, permettant la séparation spectrale des sources du champ. Le second objectif de cette thèse est la détection du Circum-Galactic Medium (CGM). Le CGM, milieu gazeux s'étendant autour de certaines galaxies, se caractérise par une signature spatialement diffuse et de faible intensité spectrale. Une méthode de détection de cette signature par test d'hypothèses est développée, basée sur une stratégie de max-test sur un dictionnaire et un apprentissage des statistiques de test sur les données. Cette méthode est ensuite étendue pour prendre en compte la structure spatiale des sources et ainsi améliorer la puissance de détection tout en conservant un contrôle global des erreurs. Les codes développés sont intégrés dans la bibliothèque logicielle du consortium MUSE afin d'être utilisables par l'ensemble de la communauté. De plus, si ces travaux sont particulièrement adaptés aux données MUSE, ils peuvent être étendus à d'autres applications dans les domaines de la séparation de sources et de la détection de sources faibles et étendues. / This work takes place in the context of the study of hyperspectral deep fields produced by the European 3D spectrograph MUSE. These fields allow to explore the young remote Universe and to study the physical and chemical properties of the first galactical and extra-galactical structures.The first part of the thesis deals with the estimation of a spectral signature for each galaxy. As MUSE is a terrestrial instrument, the atmospheric turbulences strongly degrades the spatial resolution power of the instrument thus generating spectral mixing of multiple sources. To remove this issue, data fusion approaches, based on a linear mixing model and complementary data from the Hubble Space Telescope are proposed, allowing the spectral separation of the sources.The second goal of this thesis is to detect the Circum-Galactic Medium (CGM). This CGM, which is formed of clouds of gas surrounding some galaxies, is characterized by a spatially extended faint spectral signature. To detect this kind of signal, an hypothesis testing approach is proposed, based on a max-test strategy on a dictionary. The test statistics is learned on the data. This method is then extended to better take into account the spatial structure of the targets, thus improving the detection power, while still ensuring global error control.All these developments are integrated in the software library of the MUSE consortium in order to be used by the astrophysical community.Moreover, these works can easily be extended beyond MUSE data to other application fields that need faint extended source detection and source separation methods.

Master of Science / Department of Agronomy / Walter H. Fick / Kevin Price / Caucasian bluestem [Bothriochloa bladhii (Retz) S.T. Blake] is a perennial, C4 warm-season bunchgrass that was first introduced in 1929 from Russia as a potential forage crop in the Great Plains. Due to its invasiveness and tolerance of drought and grazing pressure, Caucasian bluestem can out-compete native prairie species. Research has shown that this species, when compared to native tallgrass species in the Flint Hills of Kansas causes decreased cattle weight gains because of its poor forage quality relative to tallgrass prairie species. Traditional methods of plant data measurements and mapping are costly and time consuming. Use of remotely sensed data to map and monitor the distribution and spread of this plant would be most useful in the control of this aggressive invader. Spectroradiometer data were collected over the 2009 growing season to determine if and when Caucasian bluestem was spectrally unique from native tallgrass prairie species. Observations were made from June through September as the plants were going into a senescent state. Reflectance data were measured approximately every two weeks or when clear/near clear sky conditions prevailed. Statistical analyses for differences in spectral characteristics were conducted to determine the optimal spectral bands, indices and timing for discriminating Caucasian bluestem from native tallgrass species. Difference in reflectance for spectral reflectance of bands 760 nm, 940 nm, 1,070 nm, and 1,186 nm were found to be statistically significant on the June 17th and June 30th sampling dates. The following band ratios and indices were found to be significantly different between Caucasian bluestem and native range on the June 17th collection date: Simple Ratio, Modified Normalized Difference Index, Normalized Phaeophytinization Index, Plant Index 1, Normalized Water Difference Index, Water Band Index, Normalized Difference Nitrogen Index, and the Normalized Difference Lignin Index. Findings of this study suggest that Caucasian bluestem can be spectrally discriminated from native tallgrass prairies of the Flint Hills in Kansas if the measurements are collected in mid to late June. Statistical analyses also showed differences between treatments for percent litter, grass, and forb basal cover.

Doctor of Philosophy / Department of Food Science / Randall K. Phebus / Intervention techniques to control foodborne pathogens, and rapid identification of pathogens in food are of vital importance to ensure food safety. Therefore, the first objective of this research was to study the efficacy of radio frequency dielectric heating (RFDH) against C. sakazakii and Salmonella spp. in nonfat dry milk (NDM) at 75, 80, 85, or 90°C. Using thermal-death-time (TDT) disks, D-values of C. sakazakii in high heat (HH)- and low heat (LH)-NDM were 24.86 and 23.0 min at 75°C, 13.75 and 7.52 min at 80°C, 8.0 and 6.03 min at 85°C, and 5.57 and 5.37 min at 90°C, respectively. D-values of Salmonella spp. in HH- and LH-NDM were 23.02 and 24.94 min at 75°C, 10.45 and 12.54 min at 80°C, 8.63 and 8.68 min at 85°C, and 5.82 and 4.55 min at 90°C, respectively. The predicted (TDT) and observed (RFDH) destruction of C. sakazakii and Salmonella spp. were in agreement, indicating that the organisms' behavior was similar regardless of the heating system (conventional vs. RFDH). However, RFDH can be used as a faster and more uniform heating method for NDM to achieve the target temperatures. The second objective of this research was to study if hyperspectral imaging can be used for the rapid identification and differentiation of various foodborne pathogens. Four strains of C. sakazakii, 5 strains of Salmonella spp., 8 strains of E. coli, and 1 strain each of L. monocytogenes and S. aureus were used in the study. Principal component analysis and kNN (k-nearest neighbor) were used to develop classification models, which were then validated using a cross-validation technique. Classification accuracy of various strains within genera including C. sakazakii, Salmonella spp. and E. coli, respectively was 100%; except within C. sakazakii, strain BAA-894, and within E. coli, strains O26, O45 and O121 had 66.67% accuracy. When all strains were studied together (irrespective of their genera) for the classification, only C. sakazakii P1, E. coli O104, O111 and O145, S. Montevideo, and L. monocytogenes had 100% classification accuracy; whereas, E. coli O45 and S. Tennessee were not classified (classification accuracy of 0%).

No description available.

Assessment of leaf and canopy chlorophyll content provides information on plant physiological status; it is related to nitrogen content and hence, photosynthesis process, net primary productivity and carbon budget. In this study, a method is developed for the retrieval of total chlorophyll content (Chlorophyll a+b) per unit leaf and per unit ground area based on improved vegetation structural parameters which are derived using multispectral multi-angle remote sensing data. Structural characteristics such as clumping and gaps within a canopy affect its solar radiation absorption and distribution and impact its reflected radiance acquired by a sensor. One of the main challenges for the remote sensing community is to accurately estimate vegetation structural parameters, which inevitably influence the retrieval of leaf chlorophyll content. Multi-angle optical measurements provide a means to characterize the anisotropy of surface reflectance, which has been shown to contain information on vegetation structural characteristics. Hyperspectral optical measurements, on the other hand, provide a fine spectral resolution at the red-edge, a narrow spectral range between the red and near infra-red spectra, which is particularly useful for retrieving chlorophyll content. This study explores a new refined measurement concept of combining multi-angle and hyperspectral remote sensing that employs hyperspectral signals only in the vertical (nadir) direction and multispectral measurements in two additional (off-nadir) directions within two spectral bands, red and near infra-red (NIR). The refinement has been proposed in order to reduce the redundancy of hyperspectral data at more than one angle and to better retrieve the three-dimensional vegetation structural information by choosing the two most useful angles of measurements. To illustrate that hyperspectral data acquired at multiple angles exhibit redundancy, a radiative transfer model was used to generate off-nadir hyperspectral reflectances. It has been successfully demonstrated that the off-nadir hyperspectral simulations could be closely reconstructed based on the nadir hyperspectral reflectance and off-nadir multi-spectral reflectance in the red and NIR bands. This is shown using the Compact High-resolution Imaging Spectrometer (CHRIS) and Compact Airborne Spectrographic Imager (CASI) data acquired over a forested area in the Sudbury region (Ontario, Canada). Through intensive validation using field data, it is demonstrated that the combination of reflectances at two angles, the hotspot and darkspot, through the Normalized Difference between Hotspot and Darkspot (NDHD) index has the strongest response to changes in vegetation clumping, an important structural component of canopy. Clumping index (Ω) and Leaf Area Index (LAI) maps are generated based on previous algorithms as well as empirical relationships developed in this study. To retrieve chlorophyll content, inversion of the 5-Scale model is performed by developing Look-Up Tables (LUTs) that are based on the improved structural characteristics developed using multi-angle data. The generated clumping index and LAI maps are used in the LUTs to estimate leaf reflectance. Inversion of the leaf reflectance model, PROSPECT, is further employed to estimate chlorophyll content per unit leaf area. The estimated leaf chlorophyll contents are in good agreement with field-measured values. The refined measurement concept of combining hyperspectral with multispectral multi-angle data provides the opportunity for simultaneous retrieval of vegetation structural and biochemical parameters.

<p>Unprecedented amount of data has been collected in diverse fields such as social network, infectious disease and political science in this information explosive era. The high dimensional, complex and heterogeneous data imposes tremendous challenges on traditional statistical models. Bayesian nonparametric methods address these challenges by providing models that can fit the data with growing complexity. In this thesis, we design novel Bayesian nonparametric models on dataset from three different fields, hyperspectral images analysis, infectious disease and voting behaviors. </p><p>First, we consider analysis of noisy and incomplete hyperspectral imagery, with the objective of removing the noise and inferring the missing data. The noise statistics may be wavelength-dependent, and the fraction of data missing (at random) may be substantial, including potentially entire bands, offering the potential to significantly reduce the quantity of data that need be measured. We achieve this objective by employing Bayesian dictionary learning model, considering two distinct means of imposing sparse dictionary usage and drawing the dictionary elements from a Gaussian process prior, imposing structure on the wavelength dependence of the dictionary elements.</p><p>Second, a Bayesian statistical model is developed for analysis of the time-evolving properties of infectious disease, with a particular focus on viruses. The model employs a latent semi-Markovian state process, and the state-transition statistics are driven by three terms: ($i$) a general time-evolving trend of the overall population, ($ii$) a semi-periodic term that accounts for effects caused by the days of the week, and ($iii$) a regression term that relates the probability of infection to covariates (here, specifically, to the Google Flu Trends data).</p><p>Third, extensive information on 3 million randomly sampled United States citizens is used to construct a statistical model of constituent preferences for each U.S. congressional district. This model is linked to the legislative voting record of the legislator from each district, yielding an integrated model for constituency data, legislative roll-call votes, and the text of the legislation. The model is used to examine the extent to which legislators' voting records are aligned with constituent preferences, and the implications of that alignment (or lack thereof) on subsequent election outcomes. The analysis is based on a Bayesian nonparametric formalism, with fast inference via a stochastic variational Bayesian analysis.</p> / Dissertation

Le phénotypage consiste à caractériser les plantes et leur comportement en vue de la sélection génétique. Cette étude a évalué le potentiel de l'imagerie hyperspectrale de proximité pour répondre à ces besoins. Elle s'appuie sur le lien existant entre la physiologie des plantes et leurs propriétés optiques. Cette étude a montré qu'il est possible de retrouver la réflectance des feuilles en dépit d'un éclairage naturel variable. La procédure de correction mise en place permet de retrouver la réflectance vraie de feuilles à plat et introduit un effet additif (dû à la réflexion spéculaire), un effet multiplicatif (dû au niveau d'éclairement) et un effet non linéaire (dû aux réflexions multiples) sur les feuilles inclinées des plantes au champ. Cependant, nous avons montré également que, grâce à des pré-traitements des spectres adéquats et à la PLS (Partial Least Square regression), la concentration en azote est accessible à partir de la réflectance (400-1000~nm) de feuilles fraîches sur pied. L'étude de spectres simulés a montré que la non prise en compte des réflexions multiples dans l'étalonnage d'un modèle conduisait à une surestimation de la concentration en azote des feuilles subissant des réflexions multiples. Enfin, cette étude a illustré l'intérêt de l'imagerie hyperspectrale de proximité par rapport à la spectrométrie ponctuelle. Le fait d'avoir une image, combiné à la haute résolution spatiale permet d'obtenir des données plus représentatives de la parcelle et de calculer une vitesse de fermeture de couvert. La réalisation de cartographies d'azote permet de suivre la concentration en azote dans différents étages foliaires ou parties d'une même feuille. / Henotyping consists in characterising plants and their behavior with the aim of the genetic selection. This study estimated the potential of the close-range hyperspectral imaging to meet these needs. It leans on the link existing between plant physiology and their optical properties. This study showed that it is possible to find leaf reflectance in spite of a variable natural lighting. The developed correction procedure allows finding the true reflectance of flat leaves and introduces an additive effect (due to specular reflection), a multiplicative effect (due to illumination level) and a not linear effect (due to the multiple reflections) on inclinated leaves of plants in the field. However, we also showed that, thanks to adequate preprocessing of the spectra and to PLS (Partial Least Square regression), the nitrogen concentration is accessible from the reflectance (400-1000~nm) of fresh leaves on standing plants. The study of simulated spectra showed that the not consideration of the multiple reflections in the calibration of a model lead to an overestimation of the nitrogen concentration leaves undergoing multiple reflections. Finally, this study illustrated the interest of close-range hyperspectral imaging with regard to the punctual spectrometry. The fact of having an image, combined with the high spatial resolution allows to obtain more representative data of the plot and to calculate a speed of cover closure. Nitrogen mappings allow following the nitrogen concentration in various leaf level or parts of the same leaf.

A novel wavelet-based scheme to increase coefficient independence in hyperspectral images is introduced for lossless coding. The proposed regression wavelet analysis (RWA) uses multivariate regression to exploit the relationships among wavelettransformed components. It builds on our previous nonlinear schemes that estimate each coefficient from neighbor coefficients. Specifically, RWA performs a pyramidal estimation in the wavelet domain, thus reducing the statistical relations in the residuals and the energy of the representation compared to existing wavelet-based schemes. We propose three regression models to address the issues concerning estimation accuracy, component scalability, and computational complexity. Other suitable regression models could be devised for other goals. RWA is invertible, it allows a reversible integer implementation, and it does not expand the dynamic range. Experimental results over a wide range of sensors, such as AVIRIS, Hyperion, and Infrared Atmospheric Sounding Interferometer, suggest that RWA outperforms not only principal component analysis and wavelets but also the best and most recent coding standard in remote sensing, CCSDS-123.

The master thesis deals with subpixel classification of hyperspectral data from senzor APEX. In the first part there is research from the literature describing algorithms of the subpixel classifications and spectral characteristics of the vegetation. In the practical part there is a work focusing on the classification of the areas with the cover of Norway Spruce trees at eight areas in the Krkonoše national park. Three methods of supervised classification were used - Linear Spectral Unmixing, Support Vector Machine and Spectral Angle Mapper. Field data, spectral curves for exact trees from the eight areas obtained by the contact probe ASD FieldSpec 4 Wide-Res, were used for the extraction of endmembers of the spruces. For each research area maps of land cover were produced by means of the classification methods described above and the accuracies of the classifications were evaluated. Powered by TCPDF (www.tcpdf.org)