Hyperspectral Image Analysis through Unsupervised Deep Learning

Hyperspectral image (HSI) analysis has become an active research area in computer vision field with a wide range of applications. However, in order to yield better recognition and analysis results, we need to address two challenging issues of HSI, i.e., the existence of mixed pixels and its significantly low spatial resolution (LR). In this dissertation, spectral unmixing (SU) and hyperspectral image super-resolution (HSI-SR) approaches are developed to address these two issues with advanced deep learning models in an unsupervised fashion. A specific application, anomaly detection, is also studied, to show the importance of SU.Although deep learning has achieved the state-of-the-art performance on supervised problems, its practice on unsupervised problems has not been fully developed. To address the problem of SU, an untied denoising autoencoder is proposed to decompose the HSI into endmembers and abundances with non-negative and abundance sum-to-one constraints. The denoising capacity is incorporated into the network with a sparsity constraint to boost the performance of endmember extraction and abundance estimation.Moreover, the first attempt is made to solve the problem of HSI-SR using an unsupervised encoder-decoder architecture by fusing the LR HSI with the high-resolution multispectral image (MSI). The architecture is composed of two encoder-decoder networks, coupled through a shared decoder, to preserve the rich spectral information from the HSI network. It encourages the representations from both modalities to follow a sparse Dirichlet distribution which naturally incorporates the two physical constraints of HSI and MSI. And the angular difference between representations are minimized to reduce the spectral distortion.Finally, a novel detection algorithm is proposed through spectral unmixing and dictionary based low-rank decomposition, where the dictionary is constructed with mean-shift clustering and the coefficients of the dictionary is encouraged to be low-rank. Experimental evaluations show significant improvement on the performance of anomaly detection conducted on the abundances (through SU).The effectiveness of the proposed approaches has been evaluated thoroughly by extensive experiments, to achieve the state-of-the-art results

Hyperspectral Unmixing Overview: Geometrical, Statistical, and Sparse Regression-Based Approaches

Imaging spectrometers measure electromagnetic energy scattered in their instantaneous field view in hundreds or thousands of spectral channels with higher spectral resolution than multispectral cameras. Imaging spectrometers are therefore often referred to as hyperspectral cameras (HSCs). Higher spectral resolution enables material identification via spectroscopic analysis, which facilitates countless applications that require identifying materials in scenarios unsuitable for classical spectroscopic analysis. Due to low spatial resolution of HSCs, microscopic material mixing, and multiple scattering, spectra measured by HSCs are mixtures of spectra of materials in a scene. Thus, accurate estimation requires unmixing. Pixels are assumed to be mixtures of a few materials, called endmembers. Unmixing involves estimating all or some of: the number of endmembers, their spectral signatures, and their abundances at each pixel. Unmixing is a challenging, ill-posed inverse problem because of model inaccuracies, observation noise, environmental conditions, endmember variability, and data set size. Researchers have devised and investigated many models searching for robust, stable, tractable, and accurate unmixing algorithms. This paper presents an overview of unmixing methods from the time of Keshava and Mustard's unmixing tutorial [1] to the present. Mixing models are first discussed. Signal-subspace, geometrical, statistical, sparsity-based, and spatial-contextual unmixing algorithms are described. Mathematical problems and potential solutions are described. Algorithm characteristics are illustrated experimentally.Comment: This work has been accepted for publication in IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensin

Image Processing and Machine Learning for Hyperspectral Unmixing: An Overview and the HySUPP Python Package

Spectral pixels are often a mixture of the pure spectra of the materials, called endmembers, due to the low spatial resolution of hyperspectral sensors, double scattering, and intimate mixtures of materials in the scenes. Unmixing estimates the fractional abundances of the endmembers within the pixel. Depending on the prior knowledge of endmembers, linear unmixing can be divided into three main groups: supervised, semi-supervised, and unsupervised (blind) linear unmixing. Advances in Image processing and machine learning substantially affected unmixing. This paper provides an overview of advanced and conventional unmixing approaches. Additionally, we draw a critical comparison between advanced and conventional techniques from the three categories. We compare the performance of the unmixing techniques on three simulated and two real datasets. The experimental results reveal the advantages of different unmixing categories for different unmixing scenarios. Moreover, we provide an open-source Python-based package available at https://github.com/BehnoodRasti/HySUPP to reproduce the results

Sparse representation based hyperspectral image compression and classification

Abstract This thesis presents a research work on applying sparse representation to lossy hyperspectral image compression and hyperspectral image classification. The proposed lossy hyperspectral image compression framework introduces two types of dictionaries distinguished by the terms sparse representation spectral dictionary (SRSD) and multi-scale spectral dictionary (MSSD), respectively. The former is learnt in the spectral domain to exploit the spectral correlations, and the latter in wavelet multi-scale spectral domain to exploit both spatial and spectral correlations in hyperspectral images. To alleviate the computational demand of dictionary learning, either a base dictionary trained offline or an update of the base dictionary is employed in the compression framework. The proposed compression method is evaluated in terms of different objective metrics, and compared to selected state-of-the-art hyperspectral image compression schemes, including JPEG 2000. The numerical results demonstrate the effectiveness and competitiveness of both SRSD and MSSD approaches. For the proposed hyperspectral image classification method, we utilize the sparse coefficients for training support vector machine (SVM) and k-nearest neighbour (kNN) classifiers. In particular, the discriminative character of the sparse coefficients is enhanced by incorporating contextual information using local mean filters. The classification performance is evaluated and compared to a number of similar or representative methods. The results show that our approach could outperform other approaches based on SVM or sparse representation. This thesis makes the following contributions. It provides a relatively thorough investigation of applying sparse representation to lossy hyperspectral image compression. Specifically, it reveals the effectiveness of sparse representation for the exploitation of spectral correlations in hyperspectral images. In addition, we have shown that the discriminative character of sparse coefficients can lead to superior performance in hyperspectral image classification.EM201

Robust hyperspectral image reconstruction for scene simulation applications

This thesis presents the development of a spectral reconstruction method for multispectral (MSI) and hyperspectral (HSI) applications through an enhanced dictionary learning and spectral unmixing methodologies. Earth observation/surveillance is largely undertaken by MSI sensing such as that given by the Landsat, WorldView, Sentinel etc, however, the practical usefulness of the MSI data set is very limited. This is mainly because of the very limited number of wave bands that can be provided by the MSI imagery. One means to remedy this major shortcoming is to extend the MSI into HSI without the need of involving expensive hardware investment. Specifically, spectral reconstruction has been one of the most critical elements in applications such as Hyperspectral scene simulation. Hyperspectral scene simulation has been an important technique particularly for defence applications. Scene simulation creates a virtual scene such that modelling of the materials in the scene can be tailored freely to allow certain parameters of the model to be studied. In the defence sector this is the most cost-effective technique to allow the vulnerability of the soldiers/vehicles to be evaluated before they are deployed to a foreign ground. The simulation of a hyperspectral scene requires the details of materials in the scene, which is normally not available. Current state-of-the-art technology is trying to make use of the MSI satellite data, and to transform it into HSI for the hyperspectral scene simulation. One way to achieve this is through a reconstruction algorithm, commonly known as spectral reconstruction, which turns the MSI into HSI using an optimisation approach. The methodology that has been adopted in this thesis is the development of a robust dictionary learning to estimate the endmember (EM) robustly. Once the EM is found the abundance of materials in the scene can be subsequently estimated through a linear unmixing approach. Conventional approaches to the material allocation of most Hyperspectral scene simulator has been using the Texture Material Mapper (TMM) algorithm, which allocates materials from a spectral library (a collection of pre-compiled endmember iii iv materials) database according to the minimum spectral Euclidean distance difference to a candidate pixel of the scene. This approach has been shown (in this work) to be highly inaccurate with large scene reconstruction error. This research attempts to use a dictionary learning technique for material allocation, solving it as an optimisation problem with the objective of: (i) to reconstruct the scene as closely as possible to the ground truth with a fraction of error as that given by the TMM method, and (ii) to learn materials which are trace (2-3 times the number of species (i.e. intrinsic dimension) in the scene) cluster to ensure all material species in the scene is included for the scene reconstruction. Furthermore, two approaches complementing the goals of the learned dictionary through a rapid orthogonal matching pursuit (r-OMP) which enhances the performance of the orthogonal matching pursuit algorithm; and secondly a semi-blind approximation of the irradiance of all pixels in the scene including those in the shaded regions, have been proposed in this work. The main result of this research is the demonstration of the effectiveness of the proposed algorithms using real data set. The SCD-SOMP has been shown capable to learn both the background and trace materials even for a dictionary with small number of atoms (≈10). Also, the KMSCD method is found to be the more versatile with overcomplete (non-orthogonal) dictionary capable to learn trace materials with high scene reconstruction accuracy (2x of accuracy enhancement over that simulated using the TMM method. Although this work has achieved an incremental improvement in spectral reconstruction, however, the need of dictionary training using hyperspectral data set in this thesis has been identified as one limitation which is needed to be removed for the future direction of research

From representation learning to thematic classification - Application to hierarchical analysis of hyperspectral images

Numerous frameworks have been developed in order to analyze the increasing amount of available image data. Among those methods, supervised classification has received considerable attention leading to the development of state-of-the-art classification methods. These methods aim at inferring the class of each observation given a specific class nomenclature by exploiting a set of labeled observations. Thanks to extensive research efforts of the community, classification methods have become very efficient. Nevertheless, the results of a classification remains a highlevel interpretation of the scene since it only gives a single class to summarize all information in a given pixel. Contrary to classification methods, representation learning methods are model-based approaches designed especially to handle high-dimensional data and extract meaningful latent variables. By using physic-based models, these methods allow the user to extract very meaningful variables and get a very detailed interpretation of the considered image. The main objective of this thesis is to develop a unified framework for classification and representation learning. These two methods provide complementary approaches allowing to address the problem using a hierarchical modeling approach. The representation learning approach is used to build a low-level model of the data whereas classification is used to incorporate supervised information and may be seen as a high-level interpretation of the data. Two different paradigms, namely Bayesian models and optimization approaches, are explored to set up this hierarchical model. The proposed models are then tested in the specific context of hyperspectral imaging where the representation learning task is specified as a spectral unmixing proble

Mixture of Latent Variable Models for Remotely Sensed Image Processing

The processing of remotely sensed data is innately an inverse problem where properties of spatial processes are inferred from the observations based on a generative model. Meaningful data inversion relies on well-defined generative models that capture key factors in the relationship between the underlying physical process and the measurements. Unfortunately, as two mainstream data processing techniques, both mixture models and latent variables models (LVM) are inadequate in describing the complex relationship between the spatial process and the remote sensing data. Consequently, mixture models, such as K-Means, Gaussian Mixture Model (GMM), Linear Discriminant Analysis (LDA) and Quadratic Discriminant Analysis (QDA), characterize a class by statistics in the original space, ignoring the fact that a class can be better represented by discriminative signals in the hidden/latent feature space, while LVMs, such as Principal Component Analysis (PCA), Independent Component Analysis (ICA) and Sparse Representation (SR), seek representational signals in the whole image scene that involves multiple spatial processes, neglecting the fact that signal discovery for individual processes is more efficient. Although the combined use of mixture model and LVMs is required for remote sensing data analysis, there is still a lack of systematic exploration on this important topic in remote sensing literature. Driven by the above considerations, this thesis therefore introduces a mixture of LVM (MLVM) framework for combining the mixture models and LVMs, under which three models are developed in order to address different aspects of remote sensing data processing: (1) a mixture of probabilistic SR (MPSR) is proposed for supervised classification of hyperspectral remote sensing imagery, considering that SR is an emerging and powerful technique for feature extraction and data representation; (2) a mixture model of K “Purified” means (K-P-Means) is proposed for addressing the spectral endmember estimation, which is a fundamental issue in remote sensing data analysis; (3) and a clustering-based PCA model is introduced for SAR image denoising. Under a unified optimization scheme, all models are solved via Expectation and Maximization (EM) algorithm, by iteratively estimating the two groups of parameters, i.e., the labels of pixels and the latent variables. Experiments on simulated data and real remote sensing data demonstrate the advantages of the proposed models in the respective applications

Mineral identification using data-mining in hyperspectral infrared imagery

Les applications de l’imagerie infrarouge dans le domaine de la géologie sont principalement des applications hyperspectrales. Elles permettent entre autre l’identification minérale, la cartographie, ainsi que l’estimation de la portée. Le plus souvent, ces acquisitions sont réalisées in-situ soit à l’aide de capteurs aéroportés, soit à l’aide de dispositifs portatifs. La découverte de minéraux indicateurs a permis d’améliorer grandement l’exploration minérale. Ceci est en partie dû à l’utilisation d’instruments portatifs. Dans ce contexte le développement de systèmes automatisés permettrait d’augmenter à la fois la qualité de l’exploration et la précision de la détection des indicateurs. C’est dans ce cadre que s’inscrit le travail mené dans ce doctorat. Le sujet consistait en l’utilisation de méthodes d’apprentissage automatique appliquées à l’analyse (au traitement) d’images hyperspectrales prises dans les longueurs d’onde infrarouge. L’objectif recherché étant l’identification de grains minéraux de petites tailles utilisés comme indicateurs minéral -ogiques. Une application potentielle de cette recherche serait le développement d’un outil logiciel d’assistance pour l’analyse des échantillons lors de l’exploration minérale. Les expériences ont été menées en laboratoire dans la gamme relative à l’infrarouge thermique (Long Wave InfraRed, LWIR) de 7.7m à 11.8 m. Ces essais ont permis de proposer une méthode pour calculer l’annulation du continuum. La méthode utilisée lors de ces essais utilise la factorisation matricielle non négative (NMF). En utlisant une factorisation du premier ordre on peut déduire le rayonnement de pénétration, lequel peut ensuite être comparé et analysé par rapport à d’autres méthodes plus communes. L’analyse des résultats spectraux en comparaison avec plusieurs bibliothèques existantes de données a permis de mettre en évidence la suppression du continuum. Les expérience ayant menés à ce résultat ont été conduites en utilisant une plaque Infragold ainsi qu’un objectif macro LWIR. L’identification automatique de grains de différents matériaux tels que la pyrope, l’olivine et le quartz a commencé. Lors d’une phase de comparaison entre des approches supervisées et non supervisées, cette dernière s’est montrée plus approprié en raison du comportement indépendant par rapport à l’étape d’entraînement. Afin de confirmer la qualité de ces résultats quatre expériences ont été menées. Lors d’une première expérience deux algorithmes ont été évalués pour application de regroupements en utilisant l’approche FCC (False Colour Composite). Cet essai a permis d’observer une vitesse de convergence, jusqu’a vingt fois plus rapide, ainsi qu’une efficacité significativement accrue concernant l’identification en comparaison des résultats de la littérature. Cependant des essais effectués sur des données LWIR ont montré un manque de prédiction de la surface du grain lorsque les grains étaient irréguliers avec présence d’agrégats minéraux. La seconde expérience a consisté, en une analyse quantitaive comparative entre deux bases de données de Ground Truth (GT), nommée rigid-GT et observed-GT (rigide-GT: étiquet manuel de la région, observée-GT:étiquetage manuel les pixels). La précision des résultats était 1.5 fois meilleur lorsque l’on a utlisé la base de données observed-GT que rigid-GT. Pour les deux dernières epxérience, des données venant d’un MEB (Microscope Électronique à Balayage) ainsi que d’un microscopie à fluorescence (XRF) ont été ajoutées. Ces données ont permis d’introduire des informations relatives tant aux agrégats minéraux qu’à la surface des grains. Les résultats ont été comparés par des techniques d’identification automatique des minéraux, utilisant ArcGIS. Cette dernière a montré une performance prometteuse quand à l’identification automatique et à aussi été utilisée pour la GT de validation. Dans l’ensemble, les quatre méthodes de cette thèse représentent des méthodologies bénéfiques pour l’identification des minéraux. Ces méthodes présentent l’avantage d’être non-destructives, relativement précises et d’avoir un faible coût en temps calcul ce qui pourrait les qualifier pour être utilisée dans des conditions de laboratoire ou sur le terrain.The geological applications of hyperspectral infrared imagery mainly consist in mineral identification, mapping, airborne or portable instruments, and core logging. Finding the mineral indicators offer considerable benefits in terms of mineralogy and mineral exploration which usually involves application of portable instrument and core logging. Moreover, faster and more mechanized systems development increases the precision of identifying mineral indicators and avoid any possible mis-classification. Therefore, the objective of this thesis was to create a tool to using hyperspectral infrared imagery and process the data through image analysis and machine learning methods to identify small size mineral grains used as mineral indicators. This system would be applied for different circumstances to provide an assistant for geological analysis and mineralogy exploration. The experiments were conducted in laboratory conditions in the long-wave infrared (7.7μm to 11.8μm - LWIR), with a LWIR-macro lens (to improve spatial resolution), an Infragold plate, and a heating source. The process began with a method to calculate the continuum removal. The approach is the application of Non-negative Matrix Factorization (NMF) to extract Rank-1 NMF and estimate the down-welling radiance and then compare it with other conventional methods. The results indicate successful suppression of the continuum from the spectra and enable the spectra to be compared with spectral libraries. Afterwards, to have an automated system, supervised and unsupervised approaches have been tested for identification of pyrope, olivine and quartz grains. The results indicated that the unsupervised approach was more suitable due to independent behavior against training stage. Once these results obtained, two algorithms were tested to create False Color Composites (FCC) applying a clustering approach. The results of this comparison indicate significant computational efficiency (more than 20 times faster) and promising performance for mineral identification. Finally, the reliability of the automated LWIR hyperspectral infrared mineral identification has been tested and the difficulty for identification of the irregular grain’s surface along with the mineral aggregates has been verified. The results were compared to two different Ground Truth(GT) (i.e. rigid-GT and observed-GT) for quantitative calculation. Observed-GT increased the accuracy up to 1.5 times than rigid-GT. The samples were also examined by Micro X-ray Fluorescence (XRF) and Scanning Electron Microscope (SEM) in order to retrieve information for the mineral aggregates and the grain’s surface (biotite, epidote, goethite, diopside, smithsonite, tourmaline, kyanite, scheelite, pyrope, olivine, and quartz). The results of XRF imagery compared with automatic mineral identification techniques, using ArcGIS, and represented a promising performance for automatic identification and have been used for GT validation. In overall, the four methods (i.e. 1.Continuum removal methods; 2. Classification or clustering methods for mineral identification; 3. Two algorithms for clustering of mineral spectra; 4. Reliability verification) in this thesis represent beneficial methodologies to identify minerals. These methods have the advantages to be a non-destructive, relatively accurate and have low computational complexity that might be used to identify and assess mineral grains in the laboratory conditions or in the field