A graphics processing unit (GPU) is a specialized electronic circuit designed for digital image processing and to accelerate computer graphics, being present either as a component on a discrete graphics card or embedded on motherboards, mobile phones, personal computers, workstations, and game consoles. GPUs are increasingly being used for artificial intelligence (AI) processing due to linear algebra acceleration, which is also used extensively in graphics processing. Although there is no single definition of the term, and it may be used to describe any video display system, in modern use a GPU includes the ability to internally perform the calculations needed for various graphics tasks, like rotating and scaling 3D images, and often the additional ability to run custom programs known as shaders. This contrasts with earlier graphics controllers known as video display controllers which had no internal calculation capabilities, or blitters, which performed only basic memory movement operations. The modern GPU emerged during the 1990s, adding the ability to perform operations like drawing lines and text without CPU help, and later adding 3D functionality. Graphics functions are generally independent and this lends these tasks to being implemented on separate calculation engines. Modern GPUs include hundreds, or thousands, of calculation units. This made them useful for non-graphic calculations involving embarrassingly parallel problems due to their parallel structure. The ability of GPUs to rapidly perform vast numbers of calculations has led to their adoption in diverse fields including artificial intelligence (AI) where they excel at handling data-intensive and computationally demanding tasks. Other non-graphical uses include the training of neural networks and cryptocurrency mining. == History == === 1960s === Dedicated 3D graphics hardware dates back to graphic terminals such as the Adage AGT-30 from 1967 with analog matrix processors. In 1969 Evans & Sutherland (E&S) introduced the Line Drawing System-1 (LDS-1), which was the first all-digital system to provide matrix multiplication. Also in 1969, the low-cost graphics terminal IMLAC PDS-1 was introduced. It later saw use as an early 3D gaming machine with the likes of Maze War. === 1970s === In professional hardware, in 1972 PLATO IV system becomes operational at the University of Illinois Urbana-Champaign. Between around 1973 and 1978, several networked multiplayer wireframe 3D games are implemented and popularized by users of the system. Also in 1972, the E&S Continuous Tone 1 (CT1) "Watkins box" system (consisting of an E&S LDS-2 and Shaded Picture System) is delivered to Case Western Reserve University. It offered the first real-time Gouraud shading. In 1975, a joint effort between Evans & Sutherland Computer Corporation and the University of Utah's computer graphics department results in the first ever MOSFET video framebuffer, capable of color and smooth shading. E&S Continuous Tone 3 (CT3) system was delivered in 1977 to Lufthansa for pilot training using computer simulation. It was the first graphics system capable of real-time texture mapping. Ikonas made graphics systems with 8- and 24-bit graphics and 3D acceleration in the late 70s. Arcade system boards have used specialized 2D graphics circuits since the 1970s. In early video game hardware, RAM for frame buffers was expensive, so video chips composited data together as the display was being scanned out on the monitor. A specialized barrel shifter circuit helped the CPU animate the framebuffer graphics for various 1970s arcade video games from Midway and Taito, such as Gun Fight (1975), Sea Wolf (1976), and Space Invaders (1978). The Namco Galaxian arcade system in 1979 used specialized graphics hardware that supported RGB color, multi-colored sprites, and tilemap backgrounds. The Galaxian hardware was widely used during the golden age of arcade video games, by game companies such as Namco, Centuri, Gremlin, Irem, Konami, Midway, Nichibutsu, Sega, and Taito. The Atari 2600 in 1977 used a video shifter called the Television Interface Adaptor. Atari 8-bit computers (1979) had ANTIC, a video processor which interpreted instructions describing a "display list"—the way the scan lines map to specific bitmapped or character modes and where the memory is stored (so there did not need to be a contiguous frame buffer). 6502 machine code subroutines could be triggered on scan lines by setting a bit on a display list instruction. ANTIC also supported smooth vertical and horizontal scrolling independent of the CPU. === 1980s === In the 1980s significant advancements were made in professional 3D graphics hardware. Perhaps most impactful was the 1981 development of the Geometry Engine, a VLSI vector processor ASIC designed by Jim Clark and Marc Hannah at Stanford University. This processor is the forerunner of modern tensor cores and other similar processors marketed for graphics and AI. The Geometry Engine went on to be used in Silicon Graphics workstations for many years. Silicon Graphics's first product, shipped in November 1983, was the IRIS 1000, a terminal with hardware-accelerated 3D graphics based on the Geometry Engine. The Geometry Engine was capable of approximately 6 million operations per second. The 1981 NEC μPD7220 was the first implementation of a personal computer graphics display processor as a single large-scale integration (LSI) integrated circuit chip. This enabled the design of low-cost, high-performance video graphics cards such as those from Number Nine Visual Technology. It became the best-known GPU until the mid-1980s. It was the first fully integrated VLSI (very large-scale integration) metal–oxide–semiconductor (NMOS) graphics display processor for PCs, supported up to 1024×1024 resolution, and laid the foundations for the PC graphics market. It was used in a number of graphics cards and was licensed for clones such as the Intel 82720, the first of Intel's graphics processing units. The Williams Electronics arcade games Robotron: 2084, Joust, Sinistar, and Bubbles, all released in 1982, contain custom blitter chips for operating on 16-color bitmaps. In 1984, Hitachi released the ARTC HD63484, the first major CMOS graphics processor for personal computers. The ARTC could display up to 4K resolution when in monochrome mode. It was used in a number of graphics cards and terminals during the late 1980s. In 1985, the Amiga was released with a custom graphics chip called Agnus including a blitter for bitmap manipulation, line drawing, and area fill. It also included a coprocessor with its own simple instruction set, that was capable of manipulating graphics hardware registers in sync with the video beam (e.g. for per-scanline palette switches, sprite multiplexing, and hardware windowing), or driving the blitter. Also in 1985, IBM released the Professional Graphics Controller, designed by later to be Nvidia co-founder Curtis Priem, which was a rudimentary 3D card with 640 × 480 256-color graphics which used a dedicated CPU to draw graphics independently of the main system. It was used as the basis of cards by a number of makers (including Matrox) and its analog RGB signaling led directly to the VGA video standard. Priem later in the 80s worked on the influential Sun Microsystems GX (also known as cgsix) accelerated 2D graphics card. In 1986, Texas Instruments released the TMS34010, the first fully programmable graphics processor. It could run general-purpose code but also had a graphics-oriented instruction set. During 1990–1992, this chip became the basis of the Texas Instruments Graphics Architecture ("TIGA") Windows accelerator cards. Following in 1987, the IBM 8514 graphics system was released. It was one of the first video cards for IBM PC compatibles that implemented fixed-function 2D primitives in electronic hardware. Sharp's X68000, released in 1987, used a custom graphics chipset with a 65,536 color palette and hardware support for sprites, scrolling, and multiple playfields. It served as a development machine for Capcom's CP System arcade board. Fujitsu's FM Towns computer, released in 1989, had support for a 16,777,216 color palette. For context, IBM also introduced its Video Graphics Array (VGA) display system in 1987, with a maximum resolution of 640 × 480 pixels. Unlike 8514/A, VGA had no hardware acceleration features. In November 1988, NEC Home Electronics announced its creation of the Video Electronics Standards Association (VESA) to develop and promote a Super VGA (SVGA) computer display standard as a successor to VGA. Super VGA enabled graphics display resolutions up to 800 × 600 pixels, a 56% increase. In 1988 SGI sold IRIS workstation graphics with 10-12 Geometry Engines and introduced the IrisVision add-in board for IBM MicroChannel bus (RS/6000) based on the Geometry Engine as well. In 1988 as well, the first dedicated polygonal 3D graphics boards in arcade machines were introduced wit
Outline of databases
The following is provided as an overview of and topical guide to databases: Database – organized collection of data, today typically in digital form. The data are typically organized to model relevant aspects of reality (for example, the availability of rooms in hotels), in a way that supports processes requiring this information (for example, finding a hotel with vacancies). == What type of things are databases? == Databases can be described as all of the following: Information – sequence of symbols that can be interpreted as a message. Information can be recorded as signs, or transmitted as signals. Data – values of qualitative or quantitative variables, belonging to a set of items. Data in computing (or data processing) are often represented by a combination of items organized in rows and multiple variables organized in columns. Data are typically the results of measurements and can be visualised using graphs or images. Computer data – information in a form suitable for use with a computer. Data is often distinguished from programs. A program is a sequence of instructions that detail a task for the computer to perform. In this sense, data is everything in software that is not program code. == Types of databases == Active database – Database with event driven features Animation database – Database for storing and reusing animation fragments or motion capture data Back-end database – Organized collection of data in computingPages displaying short descriptions of redirect targets Bibliographic database – database of bibliographic records, an organized digital collection of references to published literature, including journal and newspaper articles, conference proceedings, reports, government and legal publications, patents, books, etc. Centralized database – database located and maintained in one location, unlike a distributed database. Cloud database – Database running on a cloud computing platform Collection database – collection catalog of a museum or archive implemented using a computerized database, in which the institution's objects or material are catalogued. Collective Optimization Database – open repository to enable sharing of benchmarks, data sets and optimization cases from the community, provide web services and Plug-in (computing)|plugins to analyze optimization data and predict program transformations or better hardware designs for multi-objective optimizations based on statistical and machine learning techniques provided there is enough information collected in the repository from multiple users. Configuration management database – Database used to store info on hardware and software assets Cooperative database – holds information on customers and their transactions. Current database – conventional database that stores data that is valid now. Directory – repository or database of information which is optimized for reading, under the assumption that data updates are very rare compared to data reads. Commonly, a directory supports search and browsing in addition to simple lookups. Distributed database – database in which storage devices are not all attached to a common CPU. Document-oriented database – computer program designed for storing, retrieving, and managing document-oriented, or Semi-structured model|semi structured data, information. EDA database – database specialized for the purpose of electronic design automation. Endgame tablebase – computerized database that contains precalculated exhaustive analysis of a chess endgame position. Food composition database (FCDB) – provides detailed information on the nutritional composition of foods. Full-text database – database that contains the complete text of books, dissertations, journals, magazines, newspapers or other kinds of textual documents. Also called a "complete-text database". Government database – collects personal information for various reasons (mass surveillance, Schengen Information System in the European Union, social security, statistics, etc.). Graph database – uses graph structures with nodes, edges, and properties to represent and store data. Knowledge base – special kind of database for knowledge management. A knowledge base provides a means for information to be collected, organised, shared, searched and utilised. Mobile database – can be connected to by a mobile computing device over a mobile network. Navigational database – database in which objects (or records) in it are found primarily by following references from other objects. Non-native speech database – speech database of non-native pronunciations of English. Online database – database accessible from a network, including from the Internet. Operational database – accessed by an Operational System to carry out regular operations of an organization. Parallel database – improves performance through parallelization of various operations, such as loading data, building indexes and evaluating queries. Probabilistic database – uncertain database in which the possible worlds have associated probabilities. Real-time database – processing system designed to handle workloads whose state is constantly changing (Buchmann). Relational database – collection of data items organized as a set of formally described tables from which data can be accessed easily. Spatial database – database that is optimized to store and query data that is related to objects in space, including points, lines and polygons. Temporal database – database with built-in time aspects, for example a temporal data model and a temporal version of Structured Query Language (SQL). Time series database – a time series is an associative array of numbers indexed by a datetime or a datetime range. These time series are often called profiles or curves, depending upon the market. A time series of stock prices might be called a price curve, or a time series of energy consumption might be called a load profile. Despite the disparate naming, the operations performed on them are sufficiently common as to demand special database treatment. Triplestore – purpose-built database for the storage and retrieval of triples, a triple being a data entity composed of subject-predicate-object, like "Bob is 35" or "Bob knows Fred". Very large database (VLDB) – contains an extremely high number of tuples (database rows), or occupies an extremely large physical filesystem storage space. Vulnerability database – platform aimed at collecting, maintaining, and disseminating information about discovered vulnerabilities targeting real computer systems. XLDB – Stands for "eXtremely Large Data Base". XML database – data stored in XML format, where it can be queried, exported and serialized into the desired format. == History of databases == History of databases – History of database management systems –: == Database use == Database usage requirements – Database theory – encapsulates a broad range of topics related to the study and research of the theoretical realm of databases and database management systems. Database machine – or is a computer or special hardware that stores and retrieves data from a database. Also called a "back end processor" Database server – computer program that provides database services to other computer programs or computers, as defined by the client-server model. Database application – computer program whose primary purpose is entering and retrieving information from a computer-managed database. Database management system (DBMS) – software package with computer programs that control the creation, maintenance, and use of a database. Database connection – facility in computer science that allows client software to communicate with database server software, whether on the same machine or not. Datasource – name given to the connection set up to a database from a server. The name is commonly used when creating a query to the database. The Database Source Name (DSN) does not have to be the same as the filename for the database. For example, a database file named "friends.mdb" could be set up with a DSN of "school". Then DSN "school" would then be used to refer to the database when performing a query. Data Source Name (DSN) – are data structures used to describe a connection to a data source. Sometimes known as a database source name though data sources are not limited to databases. Database administrator (DBA) – is a person responsible for the installation, configuration, upgrade, administration, monitoring and maintenance of physical databases. Lock – Comparison of database tools – (provides tables for comparing general and technical information for a number of available database administrator tools.) Database-centric architecture – software architectures in which databases play a crucial role. Also called "data-centric architecture". Intelligent database – was put forward as a system that manages information (rather than data) in a way that appears natural to users and which goes beyond simple record keeping. Two-phase locking (2PL) – is a
Determining the number of clusters in a data set
Determining the number of clusters in a data set, a quantity often labelled k as in the k-means algorithm, is a frequent problem in data clustering, and is a distinct issue from the process of actually solving the clustering problem. For a certain class of clustering algorithms (in particular k-means, k-medoids and expectation–maximization algorithm), there is a parameter commonly referred to as k that specifies the number of clusters to detect. Other algorithms such as DBSCAN and OPTICS algorithm do not require the specification of this parameter; hierarchical clustering avoids the problem altogether. The correct choice of k is often ambiguous, with interpretations depending on the shape and scale of the distribution of points in a data set and the desired clustering resolution of the user. In addition, increasing k without penalty will always reduce the amount of error in the resulting clustering, to the extreme case of zero error if each data point is considered its own cluster (i.e., when k equals the number of data points, n). Intuitively then, the optimal choice of k will strike a balance between maximum compression of the data using a single cluster, and maximum accuracy by assigning each data point to its own cluster. If an appropriate value of k is not apparent from prior knowledge of the properties of the data set, it must be chosen somehow. There are several categories of methods for making this decision. == Elbow method == The elbow method looks at the percentage of explained variance as a function of the number of clusters: One should choose a number of clusters so that adding another cluster does not give much better modeling of the data. More precisely, if one plots the percentage of variance explained by the clusters against the number of clusters, the first clusters will add much information (explain a lot of variance), but at some point the marginal gain will drop, giving an angle in the graph. The number of clusters is chosen at this point, hence the "elbow criterion". In most datasets, this "elbow" is ambiguous, making this method subjective and unreliable. Because the scale of the axes is arbitrary, the concept of an angle is not well-defined, and even on uniform random data, the curve produces an "elbow", making the method rather unreliable. Percentage of variance explained is the ratio of the between-group variance to the total variance, also known as an F-test. A slight variation of this method plots the curvature of the within group variance. The method can be traced to speculation by Robert L. Thorndike in 1953. While the idea of the elbow method sounds simple and straightforward, other methods (as detailed below) give better results. == X-means clustering == In statistics and data mining, X-means clustering is a variation of k-means clustering that refines cluster assignments by repeatedly attempting subdivision, and keeping the best resulting splits, until a criterion such as the Akaike information criterion (AIC) or Bayesian information criterion (BIC) is reached. == Information criterion approach == Another set of methods for determining the number of clusters are information criteria, such as the Akaike information criterion (AIC), Bayesian information criterion (BIC), or the deviance information criterion (DIC) — if it is possible to make a likelihood function for the clustering model. For example: The k-means model is "almost" a Gaussian mixture model and one can construct a likelihood for the Gaussian mixture model and thus also determine information criterion values. == Information–theoretic approach == Rate distortion theory has been applied to choosing k called the "jump" method, which determines the number of clusters that maximizes efficiency while minimizing error by information-theoretic standards. The strategy of the algorithm is to generate a distortion curve for the input data by running a standard clustering algorithm such as k-means for all values of k between 1 and n, and computing the distortion (described below) of the resulting clustering. The distortion curve is then transformed by a negative power chosen based on the dimensionality of the data. Jumps in the resulting values then signify reasonable choices for k, with the largest jump representing the best choice. The distortion of a clustering of some input data is formally defined as follows: Let the data set be modeled as a p-dimensional random variable, X, consisting of a mixture distribution of G components with common covariance, Γ. If we let c 1 … c K {\displaystyle c_{1}\ldots c_{K}} be a set of K cluster centers, with c X {\displaystyle c_{X}} the closest center to a given sample of X, then the minimum average distortion per dimension when fitting the K centers to the data is: d K = 1 p min c 1 … c K E [ ( X − c X ) T Γ − 1 ( X − c X ) ] {\displaystyle d_{K}={\frac {1}{p}}\min _{c_{1}\ldots c_{K}}{E[(X-c_{X})^{T}\Gamma ^{-1}(X-c_{X})]}} This is also the average Mahalanobis distance per dimension between X and the closest cluster center c X {\displaystyle c_{X}} . Because the minimization over all possible sets of cluster centers is prohibitively complex, the distortion is computed in practice by generating a set of cluster centers using a standard clustering algorithm and computing the distortion using the result. The pseudo-code for the jump method with an input set of p-dimensional data points X is: JumpMethod(X): Let Y = (p/2) Init a list D, of size n+1 Let D[0] = 0 For k = 1 ... n: Cluster X with k clusters (e.g., with k-means) Let d = Distortion of the resulting clustering D[k] = d^(-Y) Define J(i) = D[i] - D[i-1] Return the k between 1 and n that maximizes J(k) The choice of the transform power Y = ( p / 2 ) {\displaystyle Y=(p/2)} is motivated by asymptotic reasoning using results from rate distortion theory. Let the data X have a single, arbitrarily p-dimensional Gaussian distribution, and let fixed K = ⌊ α p ⌋ {\displaystyle K=\lfloor \alpha ^{p}\rfloor } , for some α greater than zero. Then the distortion of a clustering of K clusters in the limit as p goes to infinity is α − 2 {\displaystyle \alpha ^{-2}} . It can be seen that asymptotically, the distortion of a clustering to the power ( − p / 2 ) {\displaystyle (-p/2)} is proportional to α p {\displaystyle \alpha ^{p}} , which by definition is approximately the number of clusters K. In other words, for a single Gaussian distribution, increasing K beyond the true number of clusters, which should be one, causes a linear growth in distortion. This behavior is important in the general case of a mixture of multiple distribution components. Let X be a mixture of G p-dimensional Gaussian distributions with common covariance. Then for any fixed K less than G, the distortion of a clustering as p goes to infinity is infinite. Intuitively, this means that a clustering of less than the correct number of clusters is unable to describe asymptotically high-dimensional data, causing the distortion to increase without limit. If, as described above, K is made an increasing function of p, namely, K = ⌊ α p ⌋ {\displaystyle K=\lfloor \alpha ^{p}\rfloor } , the same result as above is achieved, with the value of the distortion in the limit as p goes to infinity being equal to α − 2 {\displaystyle \alpha ^{-2}} . Correspondingly, there is the same proportional relationship between the transformed distortion and the number of clusters, K. Putting the results above together, it can be seen that for sufficiently high values of p, the transformed distortion d K − p / 2 {\displaystyle d_{K}^{-p/2}} is approximately zero for K < G, then jumps suddenly and begins increasing linearly for K ≥ G. The jump algorithm for choosing K makes use of these behaviors to identify the most likely value for the true number of clusters. Although the mathematical support for the method is given in terms of asymptotic results, the algorithm has been empirically verified to work well in a variety of data sets with reasonable dimensionality. In addition to the localized jump method described above, there exists a second algorithm for choosing K using the same transformed distortion values known as the broken line method. The broken line method identifies the jump point in the graph of the transformed distortion by doing a simple least squares error line fit of two line segments, which in theory will fall along the x-axis for K < G, and along the linearly increasing phase of the transformed distortion plot for K ≥ G. The broken line method is more robust than the jump method in that its decision is global rather than local, but it also relies on the assumption of Gaussian mixture components, whereas the jump method is fully non-parametric and has been shown to be viable for general mixture distributions. == Silhouette method == The average silhouette of the data is another useful criterion for assessing the natural number of clusters. The silhouette of a data instance is a measure of how closely it is match
Apache Giraph
Apache Giraph is an Apache project to perform graph processing on big data. Giraph utilizes Apache Hadoop's MapReduce implementation to process graphs. Facebook used Giraph with some performance improvements to analyze one trillion edges using 200 machines in 4 minutes. Giraph is based on a paper published by Google about its own graph processing system called Pregel. It can be compared to other Big Graph processing libraries such as Cassovary. As of September 2023, it is no longer actively developed.
Mating pool
Mating pool is a concept used in evolutionary algorithms and means a population of parents for the next population. The mating pool is formed by candidate solutions that the selection operators deem to have the highest fitness in the current population. Solutions that are included in the mating pool are referred to as parents. Individual solutions can be repeatedly included in the mating pool, with individuals of higher fitness values having a higher chance of being included multiple times. Crossover operators are then applied to the parents, resulting in recombination of genes recognized as superior. Lastly, random changes in the genes are introduced through mutation operators, increasing the genetic variation in the gene pool. Those two operators improve the chance of creating new, superior solutions. A new generation of solutions is thereby created, the children, who will constitute the next population. Depending on the selection method, the total number of parents in the mating pool can be different to the size of the initial population, resulting in a new population that’s smaller. To continue the algorithm with an equally sized population, random individuals from the old populations can be chosen and added to the new population. At this point, the fitness value of the new solutions is evaluated. If the termination conditions are fulfilled, processes come to an end. Otherwise, they are repeated. The repetition of the steps result in candidate solutions that evolve towards the most optimal solution over time. The genes will become increasingly uniform towards the most optimal gene, a process called convergence. If 95% of the population share the same version of a gene, the gene has converged. When all the individual fitness values have reached the value of the best individual, i.e. all the genes have converged, population convergence is achieved. == Mating pool creation == Several methods can be applied to create a mating pool. All of these processes involve the selective breeding of a particular number of individuals within a population. There are multiple criteria that can be employed to determine which individuals make it into the mating pool and which are left behind. The selection methods can be split into three general types: fitness proportionate selection, ordinal based selection and threshold based selection. === Fitness proportionate selection === In the case of fitness proportionate selection, random individuals are selected to enter the pool. However, the ones with a higher level of fitness are more likely to be picked and therefore have a greater chance of passing on their features to the next generation. One of the techniques used in this type of parental selection is the roulette wheel selection. This approach divides a hypothetical circular wheel into different slots, the size of which is equal to the fitness values of each potential candidate. Afterwards, the wheel is rotated and a fixed point determines which individual gets picked. The greater the fitness value of an individual, the higher the probability of being chosen as a parent by the random spin of the wheel. Alternatively, stochastic universal sampling can be implemented. This selection method is also based on the rotation of a spinning wheel. However, in this case there is more than one fixed point and as a result all of the mating pool members will be selected simultaneously. === Ordinal based selection === The ordinal based selection methods include the tournament and ranking selection. Tournament selection involves the random selection of individuals of a population and the subsequent comparison of their fitness levels. The winners of these “tournaments” are the ones with the highest values and will be put into the mating pool as parents. In ranking selection all the individuals are sorted based on their fitness values. Then, the selection of the parents is made according to the rank of the candidates. Every individual has a chance of being chosen, but higher ranked ones are favored === Threshold based selection === The last type of selection method is referred to as the threshold based method. This includes the truncation selection method, which sorts individuals based on their phenotypic values on a specific trait and later selects the proportion of them that are within a certain threshold as parents.
Line integral convolution
In scientific visualization, line integral convolution (LIC) is a method to visualize a vector field (such as fluid motion) at high spatial resolutions. The LIC technique was first proposed by Brian Cabral and Leith Casey Leedom in 1993. In LIC, discrete numerical line integration is performed along the field lines (curves) of the vector field on a uniform grid. The integral operation is a convolution of a filter kernel and an input texture, often white noise. In signal processing, this process is known as a discrete convolution. == Overview == Traditional visualizations of vector fields use small arrows or lines to represent vector direction and magnitude. This method has a low spatial resolution, which limits the density of presentable data and risks obscuring characteristic features in the data. More sophisticated methods, such as streamlines and particle tracing techniques, can be more revealing but are highly dependent on proper seed points. Texture-based methods, like LIC, avoid these problems since they depict the entire vector field at point-like (pixel) resolution. Compared to other integration-based techniques that compute field lines of the input vector field, LIC has the advantage that all structural features of the vector field are displayed, without the need to adapt the start and end points of field lines to the specific vector field. In other words, it shows the topology of the vector field. In user testing, LIC was found to be particularly good for identifying critical points. == Algorithm == === Informal description === LIC causes output values to be strongly correlated along the field lines, but uncorrelated in orthogonal directions. As a result, the field lines contrast each other and stand out visually from the background. Intuitively, the process can be understood with the following example: the flow of a vector field can be visualized by overlaying a fixed, random pattern of dark and light paint. As the flow passes by the paint, the fluid picks up some of the paint's color, averaging it with the color it has already acquired. The result is a randomly striped, smeared texture where points along the same streamline tend to have a similar color. Other physical examples include: whorl patterns of paint, oil, or foam on a river visualisation of magnetic field lines using randomly distributed iron filings fine sand being blown by strong wind === Formal mathematical description === Although the input vector field and the result image are discretized, it pays to look at it from a continuous viewpoint. Let v {\displaystyle \mathbf {v} } be the vector field given in some domain Ω {\displaystyle \Omega } . Although the input vector field is typically discretized, we regard the field v {\displaystyle \mathbf {v} } as defined in every point of Ω {\displaystyle \Omega } , i.e. we assume an interpolation. Streamlines, or more generally field lines, are tangent to the vector field in each point. They end either at the boundary of Ω {\displaystyle \Omega } or at critical points where v = 0 {\displaystyle \mathbf {v} =\mathbf {0} } . For the sake of simplicity, critical points and boundaries are ignored in the following. A field line σ {\displaystyle {\boldsymbol {\sigma }}} , parametrized by arc length s {\displaystyle s} , is defined as d σ ( s ) d s = v ( σ ( s ) ) | v ( σ ( s ) ) | . {\displaystyle {\frac {d{\boldsymbol {\sigma }}(s)}{ds}}={\frac {\mathbf {v} ({\boldsymbol {\sigma }}(s))}{|\mathbf {v} ({\boldsymbol {\sigma }}(s))|}}.} Let σ r ( s ) {\displaystyle {\boldsymbol {\sigma }}_{\mathbf {r} }(s)} be the field line that passes through the point r {\displaystyle \mathbf {r} } for s = 0 {\displaystyle s=0} . Then the image gray value at r {\displaystyle \mathbf {r} } is set to D ( r ) = ∫ − L / 2 L / 2 k ( s ) N ( σ r ( s ) ) d s {\displaystyle D(\mathbf {r} )=\int _{-L/2}^{L/2}k(s)N({\boldsymbol {\sigma }}_{\mathbf {r} }(s))ds} where k ( s ) {\displaystyle k(s)} is the convolution kernel, N ( r ) {\displaystyle N(\mathbf {r} )} is the noise image, and L {\displaystyle L} is the length of field line segment that is followed. D ( r ) {\displaystyle D(\mathbf {r} )} has to be computed for each pixel in the LIC image. If carried out naively, this is quite expensive. First, the field lines have to be computed using a numerical method for solving ordinary differential equations, like a Runge–Kutta method, and then for each pixel the convolution along a field line segment has to be calculated. The final image will normally be colored in some way. Typically, some scalar field in Ω {\displaystyle \Omega } (like the vector length) is used to determine the hue, while the grayscale LIC output determines the brightness. Different choices of convolution kernels and random noise produce different textures; for example, pink noise produces a cloudy pattern where areas of higher flow stand out as smearing, suitable for weather visualization. Further refinements in the convolution can improve the quality of the image. === Programming description === Algorithmically, LIC takes a vector field and noise texture as input, and outputs a texture. The process starts by generating in the domain of the vector field a random gray level image at the desired output resolution. Then, for every pixel in this image, the forward and backward streamline of a fixed arc length is calculated. The value assigned to the current pixel is computed by a convolution of a suitable convolution kernel with the gray levels of all the noise pixels lying on a segment of this streamline. This creates a gray level LIC image. == Versions == === Basic === Basic LIC images are grayscale images, without color and animation. While such LIC images convey the direction of the field vectors, they do not indicate orientation; for stationary fields, this can be remedied by animation. Basic LIC images do not show the length of the vectors (or the strength of the field). === Color === The length of the vectors (or the strength of the field) is usually coded in color; alternatively, animation can be used. === Animation === LIC images can be animated by using a kernel that changes over time. Samples at a constant time from the streamline would still be used, but instead of averaging all pixels in a streamline with a static kernel, a ripple-like kernel constructed from a periodic function multiplied by a Hann function acting as a window (in order to prevent artifacts) is used. The periodic function is then shifted along the period to create an animation. === Fast LIC (FLIC) === The computation can be significantly accelerated by re-using parts of already computed field lines, specializing to a box function as convolution kernel k ( s ) {\displaystyle k(s)} and avoiding redundant computations during convolution. The resulting fast LIC method can be generalized to convolution kernels that are arbitrary polynomials. === Oriented Line Integral Convolution (OLIC) === Because LIC does not encode flow orientation, it cannot distinguish between streamlines of equal direction but opposite orientation. Oriented Line Integral Convolution (OLIC) solves this issue by using a ramp-like asymmetric kernel and a low-density noise texture. The kernel asymmetrically modulates the intensity along the streamline, producing a trace that encodes orientation; the low-density of the noise texture prevents smeared traces from overlapping, aiding readability. Fast Rendering of Oriented Line Integral Convolution (FROLIC) is a variation that approximates OLIC by rendering each trace in discrete steps instead of as a continuous smear. === Unsteady Flow LIC (UFLIC) === For time-dependent vector fields (unsteady flow), a variant called Unsteady Flow LIC has been designed that maintains the coherence of the flow animation. An interactive GPU-based implementation of UFLIC has been presented. === Parallel === Since the computation of an LIC image is expensive but inherently parallel, the process has been parallelized and, with availability of GPU-based implementations, interactive on PCs. === Multidimensional === Note that the domain Ω {\displaystyle \Omega } does not have to be a 2D domain: the method is applicable to higher dimensional domains using multidimensional noise fields. However, the visualization of the higher-dimensional LIC texture is problematic; one way is to use interactive exploration with 2D slices that are manually positioned and rotated. The domain Ω {\displaystyle \Omega } does not have to be flat either; the LIC texture can be computed also for arbitrarily shaped 2D surfaces in 3D space. == Applications == This technique has been applied to a wide range of problems since it first was published in 1993, both scientific and creative, including: Representing vector fields: visualization of steady (time-independent) flows (streamlines) visual exploration of 2D autonomous dynamical systems wind mapping water flow mapping Artistic effects for image generation and stylization: pencil drawing (auto
Spatial Analysis of Principal Components
Spatial Principal Component Analysis (sPCA) is a multivariate statistical technique that complements the traditional Principal Component Analysis (PCA) by incorporating spatial information into the analysis of genetic variation. While traditional PCA can be used to find spatial patterns, it focuses on reducing data dimensionality by identifying uncorrelated principal components that capture maximum variance, thus often lacking power to identify non-trivial spatial genetic patterns. By accounting for spatial autocorrelation, sPCA is able to uncover spatial patterns in the data and find the spatial structure of datasets where observations are either geographically or topologically linked. This statistical power improvement allows the investigation of cryptic spatial patterns of genetic variability otherwise overlooked. sPCA has been applied in various fields, including geography, ecology and genetics. == History == sPCA was introduced in 2008 by Thibaut Jombart, Sébastien Devillard, Anne-Béatrice Dufour, and D. Pontier as a spatially explicit method to investigate the spatial pattern of genetic variation among individuals or populations. In 2017, Valeria Montano and Thibaut Jombart published an alternative non-parametric test to evaluate the significance of global and local spatial genetic patterns with improved statistical power. == Details == sPCA modifies the PCA framework by integrating spatial weights, typically in the form of connectivity matrices or spatial adjacency graphs. It identifies principal components (PCs) that maximize both genentic variance and spatial autocorreation, as measured by Moran's I. These weights represent relationships between observations based on geographic distance or other spatial criteria. The method decomposes variance into two components: Global structures, correspond to positive autocorrelation, that is, reflect broad-scale spatial patterns where similar values cluster over large regions. Local structures, correspond to negative autocorrelation, that is, capture fine-scale spatial variations or localized patterns. The core of sPCA relies on the eigenanalysis of a spatially weighted covariance or correlation matrix. The spatial weight matrix can be constructed using techniques such as Delaunay triangulation, nearest-neighbor graphs, or distance-based criteria. Applications of sPCA should be used only as an explorative tool. == Applications == sPCA has been widely used in many fields, including: Ecology: To find spatial patterns in species distributions and environmental gradients. Genetics: Population structure and gene flow analysis while allowing for spatial autocorrelation considerations. Biogeography: To identify historical dispersal routes, and barriers to gene flow, providing insights into species distribution patterns and evolutionary history. == Software/Source Code == sPCA implementations are available in R in adegenet and ntbox . These tools facilitate the application of sPCA by providing functions for constructing spatial weight matrices, performing eigenanalysis, and obtaining spatial principal components in an easy-to-read form.