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Accurate, fast detection of clouds in satellite imagery has many applications, for example Numerical Weather Prediction (NWP) and climate studies of both the atmosphere and of the Earth’s surface temperature. Most operational techniques for cloud detection rely on the differences between observations of cloud and of clear-sky being more or less constant in space and in time. In reality, this is not the case - different clouds have different spectral properties, and different cloud types are more or less likely in different places and at different times, depending on atmospheric conditions and on the Earth’s surface properties. Observations of clear sky also vary in space and time, depending on atmospheric and surface conditions, and on the presence or absence of aerosol particles. The Bayesian approach adopted in this project allows pixel-specific physical information (for example from NWP) to be used to predict pixel-specific observations of clear sky. A physically-based, spatially- and temporally-specific probability that each pixel contains a cloud observation is then calculated. An advantage of this approach is that identification of ambiguously classed pixels from a probabilistic result is straightforward, in contrast to the binary result generally produced by operational techniques. This project has developed and validated the Bayesian approach to cloud detection, and has extended the range of applications for which it is suitable, achieving skills scores that match or exceed those achieved by operational methods in every case. High temperature gradients can make observations of clear sky around ocean fronts, particularly at thermal wavelengths, appear similar to cloud observations. To address this potential source of ambiguous cloud detection results, a region of imagery acquired by the AATSR sensor which was noted to contain some ocean fronts, was selected. Pixels in the region were clustered according to their spectral properties with the aim of separating pixels that correspond to different thermal regimes of the ocean. The mean spectral properties of pixels in each cluster were then processed using the Bayesian cloud detection technique and the resulting posterior probability of clear then assigned to individual pixels. Several clustering methods were investigated, and the most appropriate, which allowed pixels to be associated with multiple clusters, with a normalized vector of ‘membership strengths’, was used to conduct a case study. The distribution of final calculated probabilities of clear became markedly more bimodal when clustering was included, indicating fewer ambiguous classifications, but at the cost of some single pixel clouds being missed. While further investigations could provide a solution to this, the computational expense of the clustering method made this impractical to include in the work of this project. This new Bayesian approach to cloud detection has been successfully developed by this project to a point where it has been released under public license. Initially designed as a tool to aid retrieval of sea surface temperature from night-time imagery, this project has extended the Bayesian technique to be suitable for imagery acquired over land as well as sea, and for day-time as well as for night-time imagery. This was achieved using the land surface emissivity and surface reflectance parameter products available from the MODIS sensor. This project added a visible Radiative Transfer Model (RTM), developed at University of Edinburgh, and a kernel-based surface reflectance model, adapted here from that used by the MODIS sensor, to the cloud detection algorithm. In addition, the cloud detection algorithm was adapted to be more flexible, making its implementation for data from the SEVIRI sensor straightforward. A database of ‘difficult’ cloud and clear targets, in which a wide range of both spatial and temporal locations was represented, was provided by M´et´eo-France and used in this work to validate the extensions made to the cloud detection scheme and to compare the skill of the Bayesian approach with that of operational approaches. For night land and sea imagery, the Bayesian technique, with the improvements and extensions developed by this project, achieved skills scores 10% and 13% higher than M´et´eo-France respectively. For daytime sea imagery, the skills scores were within 1% of each other for both approaches, while for land imagery the Bayesian method achieved a 2% higher skills score. The main strength of the Bayesian technique is the physical basis of the differentiation between clear and cloud observations. Using NWP information to predict pixel-specific observations for clear-sky is relatively straightforward, but making such predictions for cloud observations is more complicated. The technique therefore relies on an empirical distribution rather than a pixel-specific prediction for cloud observations. To try and address this, this project developed a means of predicting cloudy observations through the fast forward-modelling of pixel-specific NWP information. All cloud fields in the pixel-specific NWP data were set to 0, and clouds were added to the profile at discrete intervals through the atmosphere, with cloud water- and ice- path (cwp, cip) also set to values spaced exponentially at discrete intervals up to saturation, and with cloud pixel fraction set to 25%, 50%, 75% and 100%. Only single-level, single-phase clouds were modelled, with the justification that the resulting distribution of predicted observations, once smoothed through considerations of uncertainties, is likely to include observations that would correspond to multi-phase and multi-level clouds. A fast RTM was run on the profile information for each of these individual clouds and cloud altitude-, cloud pixel fraction- and channel-specific relationships between cwp (and similarly cip) and predicted observations were calculated from the results of the RTM. These relationships were used to infer predicted observations for clouds with cwp/cip values other than those explicitly forward modelled. The parameters used to define the relationships were interpolated to define relationships for predicted observations of cloud at 10m vertical intervals through the atmosphere, with pixel coverage ranging from 25% to 100% in increments of 1%. A distribution of predicted cloud observations is then achieved without explicit forward-modelling of an impractical number of atmospheric states. Weights are applied to the representation of individual clouds within the final Probability Density Function (PDF) in order to make the distribution of predicted observations realistic, according to the pixel-specific NWP data, and to distributions seen in a global reference dataset of NWP profiles from the European Centre for Medium Range Weather Forecasting (ECMWF). The distribution is then convolved with uncertainties in forward-modelling, in the NWP data, and with sensor noise to create the final PDF in observation space, from which the conditional probability that the pixel observation corresponds to a cloud observation can be read. Although the relatively fast computational implementation of the technique was achieved, the results are disappointingly poor for the SEVIRI-acquired dataset, provided by M´et´eo-France, against which validation was carried out. This is thought to be explained by both the uncertainties in the NWP data, and the forward-modelling dependence on those uncertainties, being poorly understood, and treated too optimistically in the algorithm. Including more errors in the convolution introduces the problem of quantifying those errors (a non-trivial task), and would increase the processing time, making implementation impractical. In addition, if the uncertianties considered are too high then a PDF flatter than the empirical distribution currently used would be produced, making the technique less useful.

Satellite observations provide information on land surface processes over a large spatial extent with a frequency dependent on the satellite revisit time. These observations are not subject to the spatial limitations of the traditional point measurements and are usually collected in a global scale. With a reasonable spatial resolution and temporal frequency, the Moderate Resolution Imaging Spectroradiometer (MODIS) is one of these satellite sensors which enables the study of land-atmospheric interactions and estimation of climate variables for over a decade from remotely sensed data. This research investigated the potential of remotely sensed land surface temperature (LST) data from MODIS for air temperature (Ta) and soil moisture (SM) estimation in New Zealand and how the satellite derived parameters relate to the numerical model simulations and the in-situ ground measurements. Additionally, passive microwave SM product from the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) was applied in this research. As the first step, the MODIS LST product was validated using ground measurements at two test-sites as reference. Quality of the MODIS LST product was compared with the numerical simulations from the Weather Research and Forecasting (WRF) model. Results from the first validation site, which was located in the alpine areas of the South Island, showed that the MODIS LST has less agreement with the in-situ measurements than the WRF model simulations. It turned out that the MODIS LST is subject to sources of error, such as the effects of topography and variability in atmospheric effects over alpine areas and needs a careful pre-processing for cloud effects and outliers. On the other hand, results from the second validation site, which was located on the flat lands of the Canterbury Plains, showed significantly higher agreement with the ground truth data. Therefore, ground measurements at this site were used as the main reference data for the accuracy assessment of Ta and SM estimates. Using the MODIS LST product, Ta was estimated over a period of 10 years at several sites across New Zealand. The main question in this part of the thesis was whether to use LST series from a single MODIS pixel or the series of a spatially averaged value from multiple pixels for Ta estimation. It was found that the LST series from a single pixel can be used to model Ta with an accuracy of about ±1 ºC. The modelled Ta in this way showed r ≈ 0.80 correlation with the in-situ measurements. The Ta estimation accuracy improved to about ±0.5 ºC and the correlation to r ≈ 0.85 when LST series from spatially averaged values over a window of 9x9 to 25x25 pixels were applied. It was discussed that these improvements are due to noise reduction in the spatially averaged LST series. By comparison of LST diurnal trends from MODIS with Ta diurnal trends from hourly measurements in a weather station, it was shown that the MODIS LST has a better agreement with Ta measurements at certain times of the day with changes over day and night. After estimation of Ta, the MODIS LST was applied to derive the near-surface SM using two Apparent Thermal Inertia (ATI) functions. The objective was to find out if more daily LST observations can provide a better SM derivation. It was also aimed to identify the potential of a land-atmospheric coupled model for filling the gaps in derived SM, which were due to cloud cover. The in-situ SM measurements and rainfall data from six stations were used for validation of SM derived from the two ATI functions and simulated by the WRF model. It was shown that the ATI function based on four LST observations has a better ability to derive SM temporal profiles and is better able to detect rainfall effects. Finally, the MODIS LST was applied for spatial and temporal adjustment of the near-surface SM product from AMSR-E passive microwave observations over the South Island of New Zealand. It was shown that the adjustment technique improves AMSR-E seasonal trends and leads to a better matching with rainfall events. Additionally, a clear seasonal variability was observed in the adjusted AMSR-E SM in the spatial domain. Findings of this thesis showed that the satellite observed LST has the potential for the estimation of the land surface variables, such as the near-surface Ta and SM. This potential is greatly important on remote and alpine areas where regular measurements from weather stations are not often available. According to the results from the first validation site, however, the MODIS LST needs a careful pre-processing on those areas. The concluding chapter included a discussion of the limitations of remotely sensed data due to cloud cover, dense vegetation and rugged topography. It was concluded that the satellite observed LST has the potential for SM and Ta estimations in New Zealand. It was also found that a land-atmospheric model (such as the WRF coupled with the Noah and surface model) can be applied for filling the gaps due to cloud cover in remotely sensed variables.

Environmental factors affect fish distribution and fisher behavior. These factors are seldom included in stock assessment models, resulting in potentially inaccurate fish abundance estimates. This study determined the impact of these factors using the commercial catch rate of sauger (Sander canadensis) and walleye (Sander vitreus) in Lake Winnipeg by: (1) the use of satellite data to monitor turbidity and its impact on catch via simple linear regression and (2) the effect of environment on catch and effort using generalized linear models. No statistically significant relationship was found between catch and turbidity; a result which may be due to small sample sizes, the fish species' examined, and variable turbidity at depth. Decreased effort was correlated with harsh weather and decreased walleye catch. Increased walleye catch was correlated with low temperature and low Red River discharge. Increased sauger catch was correlated with high temperature, high cloud opacity, and average Red River discharge.

Lake surface temperature (LSTlake) can be obtained and studied in different ways: using in situ measurements, satellite imagery and modeling. Collecting spatially representative in situ data over lakes, especially for large and deep ones, is a real challenge. Satellite data products provide the opportunity to collect continuous data over very large geographic areas even in remote regions. Numerical modeling is also an approach to study the response and the role of lakes in the climate system. Satellite instruments provide spatial information unlike in situ measurements and one-dimensional (1-D) lake models that give vertical information at a single point or a few points in lakes. The advantage of remote sensing also applies to land where temperature measurements are usually taken at meteorological stations whose network is extremely sparse in northern regions. This thesis therefore examined the value of land/lake surface (skin) temperature (LSTland/lake) measurements from satellites as a complement to in situ point measurements and numerical modeling. The thesis is organized into two parts. The first part tested, two 1-D numerical models against in situ and satellite-derived LST measurements. LSTlake and ice phenology were simulated for various points at different depths on Great Slave Lake (GSL) and Great Bear Lake (GBL), two large lakes located in the Mackenzie River Basin in Canada’s Northwest Territories, using the 1-D Freshwater Lake model (FLake) and the Canadian Lake Ice Model (CLIMo) over the 2002-2010 period. Input data from three weather stations (Yellowknife, Hay River and Deline) were used for model simulations. LSTlake model results are compared to those derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Earth Observing System Terra and Aqua satellite platforms. The main goal was to examine the performance of the FLake and CLIMo models in simulating LSTlake and ice-cover under different conditions against satellite data products. Both models reveal a good agreement with daily average MODIS LSTlake from GSL and GBL on an annual basis. CLIMo showed a generally better performance than FLake for both lakes, particularly during the ice-cover season. Secondly, MODIS-derived lake and land surface temperature (LSTland/lake) products are used to analyze land and lake surface temperature patterns during the open-water and snow/ice growth seasons for the same period of time in the regions of both GBL and GSL. Land and lake temperatures from MODIS were compared with near-surface air temperature measurements obtained from nearby weather stations and with in situ temperature moorings in GBL. Results show a good agreement between satellite and in situ observations. MODIS data were found to be very useful for investigating both the spatial and temporal (seasonal) evolution of LSTland/lake over lakes and land, and for improving our understanding of thermodynamic processes (heat gains and heat loses) of the lake/land systems. Among other findings, the MODIS satellite imagery showed that the surface temperature of lakes is colder in comparison to the surrounding land from April-August and warmer from September until spring thaw.

Environmental factors affect fish distribution and fisher behavior. These factors are seldom included in stock assessment models, resulting in potentially inaccurate fish abundance estimates. This study determined the impact of these factors using the commercial catch rate of sauger (Sander canadensis) and walleye (Sander vitreus) in Lake Winnipeg by: (1) the use of satellite data to monitor turbidity and its impact on catch via simple linear regression and (2) the effect of environment on catch and effort using generalized linear models. No statistically significant relationship was found between catch and turbidity; a result which may be due to small sample sizes, the fish species' examined, and variable turbidity at depth. Decreased effort was correlated with harsh weather and decreased walleye catch. Increased walleye catch was correlated with low temperature and low Red River discharge. Increased sauger catch was correlated with high temperature, high cloud opacity, and average Red River discharge.

Fishing is a significant source of food, and constitutes an important source of income in Turkey. Due to the large extent required to analyse the distribution of fish stocks, information derived from satellites play an important role in fisheries applications. Chlorophyll concentration and sea surface temperature (SST) are the most significant parameters which define the fish habitat. The accuracy of these parameters in the Black Sea taken from two different satellites, namely Sea-viewing Wide Field-of-views Sensor (SeaWIFS) and Moderate Resolution Imaging Spectroradiometer (MODIS) are evaluated. Results indicate that both satellites give good estimates of SST but the algorithms overestimate the chlorophyll concentration values. MODIS products are used in the subsequent analyses due to their high correlation with in-situ measurements relative to SeaWIFS products. The cause of the overestimation of chlorophyll concentration is further examined and a general description of environmental variability in Black Sea is done using MODIS products. Anchovy, the most important commercial fish in Turkey, has been selected as the target specie of the study. Level 3 weekly average MODIS chlorophyll and SST products are processed using remote sensing (RS) and geographic information systems (GIS) integration to estimate potential favorable zones for pelagic fish aggregations. Two different decision rules are employed to generate fish stock maps, simple additive weigthing (SAW) and fuzzy additive weigthing (FSAW). The resultant maps are used to visualize the general distribution of Anchovy in Turkish Seas from May 2000 to May 2001. The resultant thematic fish stock maps generated by FSAW analysis represents the uncertainity in the environment better than the ones generated by SAW analysis.

[Abstract]: Since early settlement, agriculture has been one of the main industries contributing to the livelihoods of most rural communities in Australia. The wheat grain industry is Australia’s second largest agricultural export commodity, with an average value of $3.5 billion per annum. Climate variability and change, higher input costs, and world commodity markets have put increased pressure on the sustainability of the grain industry. This has lead to an increasing demand for accurate, objective and near real-time crop production information by industry. To generate such production estimates, it is essential to determine crop area planted at the desired spatial and temporal scales. However, such information at regional scale is currently not available in Australia.The aim of this study was to determine broadacre crop area estimates through the use of multi-temporal satellite imagery for major Australian winter crops. Specifically, the objectives were to: (i) assess the ability of a range of approaches to using multi-temporal Moderate Resolution Imaging Spectroradiometer (MODIS) imagery to estimate total end-of-season winter crop area; (ii) determine the discriminative ability of such remote sensing approaches in estimating planted area for wheat, barley and chickpea within a specific cropping season; (iii) develop and evaluate the methodology for determining the predictability of crop area estimates well before harvest; and (iv) validate the ability of multi-temporal MODIS approaches to determine the pre-harvest and end-of-season winter crop area estimates for different seasons and regions.MODIS enhanced vegetation index (EVI) was used as a surrogate measure for crop canopy health and architecture, for two contiguous shires in the Darling Downs region of Queensland, Australia. Multi-temporal approaches comprising principal component analysis (PCA), harmonic analysis of time series (HANTS), multi-date MODIS EVI during the crop growth period (MEVI), and two curve fitting procedures (CF1, CF2) were derived and applied. These approaches were validated against the traditional single-date approach. Early-season crop area estimates were derived through the development and application of a metric, i.e. accumulation of consecutive 16-day EVI values greater than or equal to 500, at different periods before flowering. Using ground truth data, image classification was conducted by applying supervised (maximum likelihood) and unsupervised (K-means) classification algorithms. The percent correctly classified and kappa coefficient statistics from the error matrix were used to assess pixel-scale accuracy, while shire-scale accuracy was determined using the percent error (PE) statistic. A simple linear regression of actual shire-scale data against predicted data was used to assess accuracy across regions and seasons. Actual shire-scale data was acquired from government statistical reports for the period 2000, 2001, 2003 and 2004 for the Darling Downs, and 2005 and 2006 for the entire Queensland cropping region.Results for 2003 and 2004 showed that multi-temporal HANTS, MEVI, CF1, CF2 and PCA methods achieved high overall accuracies ranging from 85% to 97% to discriminate between crops and non-crops. The accuracies for discriminating between specific crops at pixel scale were less, but still moderate, especially for wheat and barley (lowest at 57%). The HANTS approach had the smallest mean absolute percent error of 27% at shire-scale compared to other multi-temporal approaches. For early-season prediction, the 16-day EVI values greater than or equal to 500 metric showed high accuracy (94% to 98%) at a pixel scale and high R2 (0.96) for predicting total winter crop area planted.The rigour of the HANTS and the 16-day EVI values greater than or equal to 500 approaches was assessed when extrapolating over the entire Queensland cropping region for the 2005 and 2006 season. The combined early-season estimate of July and August produced high accuracy at pixel and regional scales with percent error of 8.6% and 26% below the industry estimates for 2005 and 2006 season, respectively. These satellite-derived crop area estimates were available at least four months before harvest, and deemed that such information will be highly sought after by industry in managing their risk. In discriminating among crops at pixel and regional scale, the HANTS approach showed high accuracy. Specific area estimates for wheat, barley and chickpea were, respectively, 9.9%, -5.2% and 10.9% (for 2005) and -2.8%, -78% and 64% (for 2006). Closer investigation suggested that the higher error in 2006 area estimates for barley and chickpea has emanated from the industry figures collected by the government.Area estimates of total winter crop, wheat, barley and chickpea resulted in R2 values of 0.92, 0.89, 0.82 and 0.52, when contrasted against the actual shire-scale data. A significantly high R2 (0.87) was achieved for total winter crop area estimates in Augusts across all shires for the 2006 season. Furthermore, the HANTS approach showed high accuracy in discriminating cropping area from non-cropping area and highlighted the need for accurate and up-to-date land use maps.This thesis concluded that time-series MODIS EVI imagery can be applied successfully to firstly, determine end-of-season crop area estimates at shire scale. Secondly, capturing canopy green-up through a novel metric (i.e. 16-day EVI values greater than or equal to 500) can be utilised effectively to determine early-season crop area estimates well before harvest. Finally, the extrapolability of these approaches to determine total and specific winter crop area estimates showed good utility across larger areas and seasons. Hence, it is envisaged that this technology is transferable to different regions across Australia. The utility of the remote sensing techniques developed in this study will depend on the risk agri-industry operates at within their decision and operating regimes. Trade-off between risk and value will depend on the accuracy and timing of the disseminated crop production forecast.

Environmental factors affect fish distribution and fisher behavior. These factors are seldom included in stock assessment models, resulting in potentially inaccurate fish abundance estimates. This study determined the impact of these factors using the commercial catch rate of sauger (Sander canadensis) and walleye (Sander vitreus) in Lake Winnipeg by: (1) the use of satellite data to monitor turbidity and its impact on catch via simple linear regression and (2) the effect of environment on catch and effort using generalized linear models. No statistically significant relationship was found between catch and turbidity; a result which may be due to small sample sizes, the fish species' examined, and variable turbidity at depth. Decreased effort was correlated with harsh weather and decreased walleye catch. Increased walleye catch was correlated with low temperature and low Red River discharge. Increased sauger catch was correlated with high temperature, high cloud opacity, and average Red River discharge. / October 2006

The goal of this research was to construct a time series of accurate chlorophyll-a concentration for the Strait of Georgia (SoG), Canada, using an improved atmospheric correction scheme and workflow for the Moderate Resolution Imaging Spectroradiometer AQUA (MODIS) satellite instrument to describe the chla dynamics and spring bloom phenology in the SoG. In situ radiometric samples were acquired via Aerosol Robotic Network (AERONET), and hyperspectral data collected from a Hyperspectral Surface Acquisition System (HyperSAS) to assess three potential atmospheric correction schemes. Water property samples including total suspended material (TSM), chromophoric dissolved organic matter (CDOM), and chlorophyll concentrations (chla) were collected to further assess atmospheric corrections and the applied ‘Ocean Color 3 Modis’ (OC3M) standard chlorophyll algorithm. Regression, Absolute percentage difference (APD), Relative Percentage difference (RPD), and Root mean squared error (RMSE) analysis revealed the most appropriate method to be the ‘Management Unit of the North Seas Mathematical Models’ (MUMM) using the shortwave infrared spectrum (SWIR) to determine NIR-derived aerosol model. This method was used to construct a time series (July 2002-June 2014) of daily chlorophyll maps for all available imagery. Files were spatially binned into 8-day composites for the North and Central SoG where a modified threshold-based definition was used to determine the start of the spring phytoplankton bloom period, as well as timing of maxima and duration of the largest spring bloom. Results indicate Central SoG start dates range from late February to late April, with an average start date at the last week of March. These results compare favorably to Hindcast predictive modelling of bloom start dates. The Northern SoG bloom phenology starts on average 9 days earlier, and experiences lower chlorophyll-a magnitudes. Hierarchical clustering with correlation similarity of spring seasons indicate 2008 and 2007 were anomalous, while 2009 and 2012 were the most correlated for blooms occurring in the spring season. / Graduate / 0366 / 0416 / 0752 / 0368 / carswell@uvic.ca