This is a list of software and programming tools for the Ruby programming language, which includes libraries, web frameworks, implementations, tools, and related projects. == Web tools == Capistrano (software) – remote server automation tool Mongrel – Ruby web server Rack – interface between web servers and web applications Ruby on Rails – full-stack web application framework Sinatra – lightweight Ruby web application framework Spree Commerce – e-commerce platform WEBrick – Ruby HTTP server toolkit == Libraries == BioRuby – bioinformatics and computational biology library for Ruby Bogus – Ruby library for creating reliable test doubles with contract verification ERuby – embedded Ruby templating EventMachine – event-driven I/O library Factory Bot – test fixtures library Fat comma – Ruby library for JSON-like hash syntax Geocoder – Ruby library for geocoding and reverse geocoding addresses Haml – HTML templating engine Markaby – HTML generation via Ruby Nokogiri – XML/HTML parsing library RSpec – behavior-driven testing framework for Ruby RubyGems – package manager for Ruby libraries and applications Sass – CSS preprocessor Sidekiq – background job framework for Ruby, used to handle asynchronous tasks. Uconv – Unicode text conversion library Watir – web application testing framework == Ruby implementations == HotRuby – Ruby interpreter implemented in JavaScript, enabling Ruby code to run in web browsers. IronRuby – Ruby for .NET platform JRuby – Ruby on the Java Virtual Machine MacRuby – Ruby implementation for macOS Mod ruby – Apache module that embeds the Ruby interpreter to improve performance of Ruby web applications Mruby – lightweight Ruby interpreter Rubinius – alternative Ruby implementation, based loosely on the Smalltalk-80 Blue Book design. Ruby MRI – the standard Ruby interpreter YARV – "Yet Another Ruby VM," the bytecode interpreter used in modern Ruby implementations == Tools == Homebrew – package manager for macOS and Linux written in Ruby Pry – interactive Ruby shell Rake – build and task management Ruby Version Manager – environment manager RubyCocoa – bridge between Ruby and Cocoa RubyForge – project hosting site RubyMotion – for iOS/macOS development RubySpec – language specification tests == Integrated Development Environments == Aptana Studio — integrated RadRails plugin for Ruby on Rails development Eclipse DLTK Ruby Plugin — Ruby development plugin for Eclipse Eric — open-source Python-based IDE with Ruby support Komodo IDE — commercial cross-platform IDE with Ruby support RubyMine — commercial IDE for Ruby and Rails by JetBrains SlickEdit — commercial cross-platform IDE with Ruby support == List of websites using Ruby on Rails == Airbnb Basecamp Diaspora – decentralized social network application built with Ruby on Rails Discourse – open-source discussion platform built with Ruby on Rails Fiverr GitHub Hulu Shopify SoundCloud Twitch Zendesk
The Cancer Imaging Archive
The Cancer Imaging Archive (TCIA) is an open-access database of medical images for cancer research. The site is funded by the National Cancer Institute's (NCI) Cancer Imaging Program, and the contract is operated by the University of Arkansas for Medical Sciences. Data within the archive is organized into collections which typically share a common cancer type and/or anatomical site. The majority of the data consists of CT, MRI, and nuclear medicine (e.g. PET) images stored in DICOM format, but many other types of supporting data are also provided or linked to, in order to enhance research utility. All data are de-identified in order to comply with the Health Insurance Portability and Accountability Act and National Institutes of Health data sharing policies. TCIA resources are intended to support: Development of computer aided diagnosis methods (quantitative imaging) Evaluation of unbiased science reproducibility by acceptable standard statistical methods Research on correlation of clinical diagnostic medical images with digital microscopic histological images Exploratory biomarker research for which imaging is a key element Collaboration between cross-disciplinary investigators where imaging is crucial to research on tumor heterogeneity, between patients and within the tumor; tissue temporal response tracking - objective measurements of tumor progression; imaging genomics and Big Data linkages and analysis (clinical, histo-pathology, genomics) TCIA is recognized as a recommended repository for the Scientific Data, PLOS One, and F1000Research journals. It is also listed in the Registry of Research Data Repositories. == History == Prior to the creation of TCIA, the NCI funded development of the National Biomedical Imaging Archive. NBIA is an open-source Web application which was designed to allow the storage and query of DICOM images. TCIA was subsequently initiated in December 2010 to expand data sharing activities by funding a service component which would help address the technical and policy challenges associated with medical imaging research. TCIA leverages open-source tools such as NBIA and Clinical Trials Processor in order to provide its services. == Organization of the archive == The site content is organized into five categories: About Us - Provides a general overview of the site the organizations responsible for operating it. Share Your Data - Provides an overview of how to apply to upload data to the archive. Access the Archive - Provides information about the available data, methods for accessing that data and system usage metrics. Research Activities - Provides information about major research initiatives being conducted using TCIA data as well as information about publication guidelines. Help - Provides information about how to get support using the archive as well as documentation and data usage policies. == Methods for accessing data == Most collections on the Cancer Imaging Archive can be accessed without an account, but a few are restricted to specific users and therefore require an account to access them. TCIA has several ways to browse, filter, and download data. They include: Downloading the entire contents of a collection in bulk Leveraging the NBIA application to filter or search within or across collections Utilizing the RESTful Application programming interface to filter or search within or across collections === Browsing, bulk downloading and access to supporting data === The home page includes a list of all available collections. Basic information about the data such as the cancer type, cancer location, modalities, and number of subjects are also provided. Clicking on a collection name presents a page which describes the data including its original research purpose, how the data were generated, and how it might be useful to other TCIA users. For example, doi:10.7937/K9/TCIA.2015.L4FRET6Z describes the NSCLC-Radiomics-Genomics Collection. In the lower section of the page there are links to search or download the images and any available supporting data in the Data Access tab. Additional tabs provide information about data versions and how to cite the data if used in publications. Many collections contain additional data types such as genomics, patient demographics, treatment details, and expert analyses of the images. This data is usually only found by browsing the collection pages as opposed to searching in NBIA or using the API. === Filtering or searching with NBIA === On each Collection page and also in the main menu of the site there are links to "Search TCIA". This will load the NBIA application which allows simple, advanced and free text searches. Search results follow the conventional DICOM hierarchy of patient -> study -> series. TCIA provides comprehensive documentation on the various features of the NBIA software. === RESTful API === A number of search and download commands are also available through the API. New iterations on the API are released as new versions, so that existing applications developed against older versions of the API continue to function. == Research activities == A list of known publications based on TCIA data is maintained as a convenience to researchers who might want to investigate how it has been used previously. In addition to peer-reviewed publications there are also several major research initiatives described in the Research Activities section of the site. === The CIP TCGA Radiology Initiative for Radiogenomics Research === A large number of collections contain subjects which were analyzed as part of the NIH/NHGRI database known as The Cancer Genome Atlas (TCGA). This offers researchers the ability to correlate clinical images using shared unique identifiers each study that has in TCGA extensive genomic analysis, digital pathology slides and bulk download of individual demographic data and clinical data. A multi-institutional network of investigators volunteering their time is using the data to develop methods to determine prognosis or predict the response to therapy. TCGA collections are designated by nomenclature shared by the TCGA Data Portal (e.g.: TCGA-BRCA, TCGA-GBM, etc). They are subject to a special publication policy which is unique from the other public data on TCIA. === Challenge competitions === TCIA also provides specific data sets used for "Challenge" competitions such as international digital image-focused professional societies like MICCAI, SPIE, or ISBI. A directory of previous and upcoming challenges is maintained on the site. === Digital object identifiers === To facilitate data sharing, many publications encourage authors to include data citations to the data that the authors used in creating the results described in their scholarly papers. In addition, new journals are now available for describing data collections outright (e.g., Nature Scientific Data). TCIA assigns digital object identifiers (DOIs) to all collections when they are submitted, and also has the ability to create persistent identifiers linked to subsets of data held within TCIA that authors may use for data citations in their scholarly papers.
Uniform convergence in probability
Uniform convergence in probability is a form of convergence in probability in statistical asymptotic theory and probability theory. It means that, under certain conditions, the empirical frequencies of all events in a certain event-family uniformly converge to their theoretical probabilities. Uniform convergence in probability has applications to statistics as well as machine learning as part of statistical learning theory. Specifically, the Glivenko-Cantelli theorem and the homonymous classes of functions are fundamentally related to uniform convergence. The law of large numbers says that, for each single event A {\displaystyle A} , its empirical frequency in a sequence of independent trials converges (with high probability) to its theoretical probability. In many application however, the need arises to judge simultaneously the probabilities of events of an entire class S {\displaystyle S} from one and the same sample. Moreover, it, is required that the relative frequency of the events converge to the probability uniformly over the entire class of events S {\displaystyle S} . The Uniform Convergence Theorem gives a sufficient condition for this convergence to hold. Roughly, if the event-family is sufficiently simple (its VC dimension is sufficiently small) then uniform convergence holds. == Definitions == For a class of predicates H {\displaystyle H} defined on a set X {\displaystyle X} and a set of samples x = ( x 1 , x 2 , … , x m ) {\displaystyle x=(x_{1},x_{2},\dots ,x_{m})} , where x i ∈ X {\displaystyle x_{i}\in X} , the empirical frequency of h ∈ H {\displaystyle h\in H} on x {\displaystyle x} is Q ^ x ( h ) = 1 m | { i : 1 ≤ i ≤ m , h ( x i ) = 1 } | . {\displaystyle {\widehat {Q}}_{x}(h)={\frac {1}{m}}|\{i:1\leq i\leq m,h(x_{i})=1\}|.} The theoretical probability of h ∈ H {\displaystyle h\in H} is defined as Q P ( h ) = P { y ∈ X : h ( y ) = 1 } . {\displaystyle Q_{P}(h)=P\{y\in X:h(y)=1\}.} The Uniform Convergence Theorem states, roughly, that if H {\displaystyle H} is "simple" and we draw samples independently (with replacement) from X {\displaystyle X} according to any distribution P {\displaystyle P} , then with high probability, the empirical frequency will be close to its expected value, which is the theoretical probability. Here "simple" means that the Vapnik–Chervonenkis dimension of the class H {\displaystyle H} is small relative to the size of the sample. In other words, a sufficiently simple collection of functions behaves roughly the same on a small random sample as it does on the distribution as a whole. The Uniform Convergence Theorem was first proved by Vapnik and Chervonenkis using the concept of growth function. == Uniform Convergence Theorem == The statement of the Uniform Convergence Theorem is as follows: If H {\displaystyle H} is a set of { 0 , 1 } {\displaystyle \{0,1\}} -valued functions defined on a set X {\displaystyle X} and P {\displaystyle P} is a probability distribution on X {\displaystyle X} then for ε > 0 {\displaystyle \varepsilon >0} and m {\displaystyle m} a positive integer, we have: P m { | Q P ( h ) − Q x ^ ( h ) | ≥ ε for some h ∈ H } ≤ 4 Π H ( 2 m ) e − ε 2 m / 8 . {\displaystyle P^{m}\{|Q_{P}(h)-{\widehat {Q_{x}}}(h)|\geq \varepsilon {\text{ for some }}h\in H\}\leq 4\Pi _{H}(2m)e^{-\varepsilon ^{2}m/8}.} In the above, for any x ∈ X m , {\displaystyle x\in X^{m},} Q P ( h ) = P { ( y ∈ X : h ( y ) = 1 } , {\displaystyle Q_{P}(h)=P\{(y\in X:h(y)=1\},} Q ^ x ( h ) = 1 m | { i : 1 ≤ i ≤ m , h ( x i ) = 1 } | {\displaystyle {\widehat {Q}}_{x}(h)={\frac {1}{m}}|\{i:1\leq i\leq m,h(x_{i})=1\}|} and | x | = m . {\displaystyle |x|=m.} P m {\displaystyle P^{m}} indicates that the probability is taken over x {\displaystyle x} consisting of m {\displaystyle m} i.i.d. draws from the distribution P . {\displaystyle P.} Finally, the growth function Π H {\displaystyle \Pi _{H}} is defined in the following way, for any { 0 , 1 } {\displaystyle \{0,1\}} -valued functions H {\displaystyle H} over X {\displaystyle X} and for any natural number m {\displaystyle m} : Π H ( m ) = max | { h ∩ D : D ⊆ X , | D | = m , h ∈ H } | . {\displaystyle \Pi _{H}(m)=\max |\{h\cap D:D\subseteq X,|D|=m,h\in H\}|.} From the point of view of Learning Theory one can consider H {\displaystyle H} to be the Concept/Hypothesis class defined over the instance set X {\displaystyle X} . Crucially, the Sauer–Shelah lemma implies that Π H ( m ) ≤ m d {\displaystyle \Pi _{H}(m)\leq m^{d}} , where d {\displaystyle d} is the VC dimension of H {\displaystyle H} . == Proof of the Uniform Convergence Theorem == and are the sources of the proof below. Before we get into the details of the proof of the Uniform Convergence Theorem we will present a high level overview of the proof. Symmetrization: We transform the problem of analyzing | Q P ( h ) − Q ^ x ( h ) | ≥ ε {\displaystyle |Q_{P}(h)-{\widehat {Q}}_{x}(h)|\geq \varepsilon } into the problem of analyzing | Q ^ r ( h ) − Q ^ s ( h ) | ≥ ε / 2 {\displaystyle |{\widehat {Q}}_{r}(h)-{\widehat {Q}}_{s}(h)|\geq \varepsilon /2} , where r {\displaystyle r} and s {\displaystyle s} are i.i.d samples of size m {\displaystyle m} drawn according to the distribution P {\displaystyle P} . One can view r {\displaystyle r} as the original randomly drawn sample of length m {\displaystyle m} , while s {\displaystyle s} may be thought as the testing sample which is used to estimate Q P ( h ) {\displaystyle Q_{P}(h)} . Permutation: Since r {\displaystyle r} and s {\displaystyle s} are picked identically and independently, so swapping elements between them will not change the probability distribution on r {\displaystyle r} and s {\displaystyle s} . So, we will try to bound the probability of | Q ^ r ( h ) − Q ^ s ( h ) | ≥ ε / 2 {\displaystyle |{\widehat {Q}}_{r}(h)-{\widehat {Q}}_{s}(h)|\geq \varepsilon /2} for some h ∈ H {\displaystyle h\in H} by considering the effect of a specific collection of permutations of the joint sample x = r | | s {\displaystyle x=r||s} . Specifically, we consider permutations σ ( x ) {\displaystyle \sigma (x)} which swap x i {\displaystyle x_{i}} and x m + i {\displaystyle x_{m+i}} in some subset of 1 , 2 , . . . , m {\displaystyle {1,2,...,m}} . The symbol r | | s {\displaystyle r||s} means the concatenation of r {\displaystyle r} and s {\displaystyle s} . Reduction to a finite class: We can now restrict the function class H {\displaystyle H} to a fixed joint sample and hence, if H {\displaystyle H} has finite VC Dimension, it reduces to the problem to one involving a finite function class. We present the technical details of the proof. It should be stressed that this proof glosses over details like the measurability of the events V {\displaystyle V} and R {\displaystyle R} ; measurability is granted in the case of H {\displaystyle H} being finite or countable, but this is not normally the case in standard applications of the theorem (e.g. for statistical learning theory or to prove the Glivenko-Cantelli theorem). To get measurability, one needs to use a notion of separability of the underlying space, possibly related to H {\displaystyle H} . === Symmetrization === Lemma: Let V = { x ∈ X m : | Q P ( h ) − Q ^ x ( h ) | ≥ ε for some h ∈ H } {\displaystyle V=\{x\in X^{m}:|Q_{P}(h)-{\widehat {Q}}_{x}(h)|\geq \varepsilon {\text{ for some }}h\in H\}} and R = { ( r , s ) ∈ X m × X m : | Q r ^ ( h ) − Q ^ s ( h ) | ≥ ε / 2 for some h ∈ H } . {\displaystyle R=\{(r,s)\in X^{m}\times X^{m}:|{\widehat {Q_{r}}}(h)-{\widehat {Q}}_{s}(h)|\geq \varepsilon /2{\text{ for some }}h\in H\}.} Then for m ≥ 2 ε 2 {\displaystyle m\geq {\frac {2}{\varepsilon ^{2}}}} , P m ( V ) ≤ 2 P 2 m ( R ) {\displaystyle P^{m}(V)\leq 2P^{2m}(R)} . Proof: By the triangle inequality, if | Q P ( h ) − Q ^ r ( h ) | ≥ ε {\displaystyle |Q_{P}(h)-{\widehat {Q}}_{r}(h)|\geq \varepsilon } and | Q P ( h ) − Q ^ s ( h ) | ≤ ε / 2 {\displaystyle |Q_{P}(h)-{\widehat {Q}}_{s}(h)|\leq \varepsilon /2} then | Q ^ r ( h ) − Q ^ s ( h ) | ≥ ε / 2 {\displaystyle |{\widehat {Q}}_{r}(h)-{\widehat {Q}}_{s}(h)|\geq \varepsilon /2} . Therefore, P 2 m ( R ) ≥ P 2 m { ∃ h ∈ H , | Q P ( h ) − Q ^ r ( h ) | ≥ ε and | Q P ( h ) − Q ^ s ( h ) | ≤ ε / 2 } = ∫ V P m { s : ∃ h ∈ H , | Q P ( h ) − Q ^ r ( h ) | ≥ ε and | Q P ( h ) − Q ^ s ( h ) | ≤ ε / 2 } d P m ( r ) = A {\displaystyle {\begin{aligned}&P^{2m}(R)\\[5pt]\geq {}&P^{2m}\{\exists h\in H,|Q_{P}(h)-{\widehat {Q}}_{r}(h)|\geq \varepsilon {\text{ and }}|Q_{P}(h)-{\widehat {Q}}_{s}(h)|\leq \varepsilon /2\}\\[5pt]={}&\int _{V}P^{m}\{s:\exists h\in H,|Q_{P}(h)-{\widehat {Q}}_{r}(h)|\geq \varepsilon {\text{ and }}|Q_{P}(h)-{\widehat {Q}}_{s}(h)|\leq \varepsilon /2\}\,dP^{m}(r)\\[5pt]={}&A\end{aligned}}} since r {\displaystyle r} and s {\displaystyle s} are independent. Now for r ∈ V {\displaystyle r\in V} fix an h ∈ H {\displaystyle h\in H} such that | Q P ( h ) − Q ^ r ( h ) | ≥ ε {\displaystyle |Q_{P}(h)-{\widehat {Q}}_{r}(h)|\geq \varepsilon } . For this h {\displaystyle h} , we shall
Scale-space axioms
In image processing and computer vision, a scale space framework can be used to represent an image as a family of gradually smoothed images. This framework is very general and a variety of scale space representations exist. A typical approach for choosing a particular type of scale space representation is to establish a set of scale-space axioms, describing basic properties of the desired scale-space representation and often chosen so as to make the representation useful in practical applications. Once established, the axioms narrow the possible scale-space representations to a smaller class, typically with only a few free parameters. A set of standard scale space axioms, discussed below, leads to the linear Gaussian scale-space, which is the most common type of scale space used in image processing and computer vision. == Scale space axioms for the linear scale-space representation == The linear scale space representation L ( x , y , t ) = ( T t f ) ( x , y ) = g ( x , y , t ) ∗ f ( x , y ) {\displaystyle L(x,y,t)=(T_{t}f)(x,y)=g(x,y,t)f(x,y)} of signal f ( x , y ) {\displaystyle f(x,y)} obtained by smoothing with the Gaussian kernel g ( x , y , t ) {\displaystyle g(x,y,t)} satisfies a number of properties 'scale-space axioms' that make it a special form of multi-scale representation: linearity T t ( a f + b h ) = a T t f + b T t h {\displaystyle T_{t}(af+bh)=aT_{t}f+bT_{t}h} where f {\displaystyle f} and h {\displaystyle h} are signals while a {\displaystyle a} and b {\displaystyle b} are constants, shift invariance T t S ( Δ x , Δ y ) f = S ( Δ x , Δ y ) T t f {\displaystyle T_{t}S_{(\Delta x,\Delta _{y})}f=S_{(\Delta x,\Delta _{y})}T_{t}f} where S ( Δ x , Δ y ) {\displaystyle S_{(\Delta x,\Delta _{y})}} denotes the shift (translation) operator ( S ( Δ x , Δ y ) f ) ( x , y ) = f ( x − Δ x , y − Δ y ) {\displaystyle (S_{(\Delta x,\Delta _{y})}f)(x,y)=f(x-\Delta x,y-\Delta y)} semi-group structure g ( x , y , t 1 ) ∗ g ( x , y , t 2 ) = g ( x , y , t 1 + t 2 ) {\displaystyle g(x,y,t_{1})g(x,y,t_{2})=g(x,y,t_{1}+t_{2})} with the associated cascade smoothing property L ( x , y , t 2 ) = g ( x , y , t 2 − t 1 ) ∗ L ( x , y , t 1 ) {\displaystyle L(x,y,t_{2})=g(x,y,t_{2}-t_{1})L(x,y,t_{1})} existence of an infinitesimal generator A {\displaystyle A} ∂ t L ( x , y , t ) = ( A L ) ( x , y , t ) {\displaystyle \partial _{t}L(x,y,t)=(AL)(x,y,t)} non-creation of local extrema (zero-crossings) in one dimension, non-enhancement of local extrema in any number of dimensions ∂ t L ( x , y , t ) ≤ 0 {\displaystyle \partial _{t}L(x,y,t)\leq 0} at spatial maxima and ∂ t L ( x , y , t ) ≥ 0 {\displaystyle \partial _{t}L(x,y,t)\geq 0} at spatial minima, rotational symmetry g ( x , y , t ) = h ( x 2 + y 2 , t ) {\displaystyle g(x,y,t)=h(x^{2}+y^{2},t)} for some function h {\displaystyle h} , scale invariance g ^ ( ω x , ω y , t ) = h ^ ( ω x φ ( t ) , ω x φ ( t ) ) {\displaystyle {\hat {g}}(\omega _{x},\omega _{y},t)={\hat {h}}({\frac {\omega _{x}}{\varphi (t)}},{\frac {\omega _{x}}{\varphi (t)}})} for some functions φ {\displaystyle \varphi } and h ^ {\displaystyle {\hat {h}}} where g ^ {\displaystyle {\hat {g}}} denotes the Fourier transform of g {\displaystyle g} , positivity g ( x , y , t ) ≥ 0 {\displaystyle g(x,y,t)\geq 0} , normalization ∫ x = − ∞ ∞ ∫ y = − ∞ ∞ g ( x , y , t ) d x d y = 1 {\displaystyle \int _{x=-\infty }^{\infty }\int _{y=-\infty }^{\infty }g(x,y,t)\,dx\,dy=1} . In fact, it can be shown that the Gaussian kernel is a unique choice given several different combinations of subsets of these scale-space axioms: most of the axioms (linearity, shift-invariance, semigroup) correspond to scaling being a semigroup of shift-invariant linear operator, which is satisfied by a number of families integral transforms, while "non-creation of local extrema" for one-dimensional signals or "non-enhancement of local extrema" for higher-dimensional signals are the crucial axioms which relate scale-spaces to smoothing (formally, parabolic partial differential equations), and hence select for the Gaussian. The Gaussian kernel is also separable in Cartesian coordinates, i.e. g ( x , y , t ) = g ( x , t ) g ( y , t ) {\displaystyle g(x,y,t)=g(x,t)\,g(y,t)} . Separability is, however, not counted as a scale-space axiom, since it is a coordinate dependent property related to issues of implementation. In addition, the requirement of separability in combination with rotational symmetry per se fixates the smoothing kernel to be a Gaussian. There exists a generalization of the Gaussian scale-space theory to more general affine and spatio-temporal scale-spaces. In addition to variabilities over scale, which original scale-space theory was designed to handle, this generalized scale-space theory also comprises other types of variabilities, including image deformations caused by viewing variations, approximated by local affine transformations, and relative motions between objects in the world and the observer, approximated by local Galilean transformations. In this theory, rotational symmetry is not imposed as a necessary scale-space axiom and is instead replaced by requirements of affine and/or Galilean covariance. The generalized scale-space theory leads to predictions about receptive field profiles in good qualitative agreement with receptive field profiles measured by cell recordings in biological vision. In the computer vision, image processing and signal processing literature there are many other multi-scale approaches, using wavelets and a variety of other kernels, that do not exploit or require the same requirements as scale space descriptions do; please see the article on related multi-scale approaches. There has also been work on discrete scale-space concepts that carry the scale-space properties over to the discrete domain; see the article on scale space implementation for examples and references.
Hard sigmoid
In artificial intelligence, especially computer vision and artificial neural networks, a hard sigmoid is non-smooth function used in place of a sigmoid function. These retain the basic shape of a sigmoid, rising from 0 to 1, but using simpler functions, especially piecewise linear functions or piecewise constant functions. These are preferred where speed of computation is more important than precision. == Examples == The most extreme examples are the sign function or Heaviside step function, which go from −1 to 1 or 0 to 1 (which to use depends on normalization) at 0. Other examples include the Theano library, which provides two approximations: ultra_fast_sigmoid, which is a multi-part piecewise approximation and hard_sigmoid, which is a 3-part piecewise linear approximation (output 0, line with slope 0.2, output 1).
Convolution
In mathematics (in particular, functional analysis), convolution is a mathematical operation on two functions f {\displaystyle f} and g {\displaystyle g} that produces a third function f ∗ g {\displaystyle fg} , as the integral of the product of the two functions after one is reflected about the y-axis and shifted. The term convolution refers to both the resulting function and to the process of computing it. The integral is evaluated for all values of shift, producing the convolution function. The choice of which function is reflected and shifted before the integral does not change the integral result (see commutativity). Graphically, it expresses how the 'shape' of one function is modified by the other. Some features of convolution are similar to cross-correlation: for real-valued functions, of a continuous or discrete variable, convolution f ∗ g {\displaystyle fg} differs from cross-correlation f ⋆ g {\displaystyle f\star g} only in that either f ( x ) {\displaystyle f(x)} or g ( x ) {\displaystyle g(x)} is reflected about the y-axis in convolution; thus it is a cross-correlation of g ( − x ) {\displaystyle g(-x)} and f ( x ) {\displaystyle f(x)} , or f ( − x ) {\displaystyle f(-x)} and g ( x ) {\displaystyle g(x)} . For complex-valued functions, the cross-correlation operator is the adjoint of the convolution operator. Convolution has applications that include probability, statistics, acoustics, spectroscopy, signal processing and image processing, computer vision and human vision, geophysics, engineering, physics, and differential equations. The convolution can be defined for functions on Euclidean space and other groups (as algebraic structures). For example, periodic functions, such as the discrete-time Fourier transform, can be defined on a circle and convolved by periodic convolution. (See row 18 at DTFT § Properties.) A discrete convolution can be defined for functions on the set of integers. Generalizations of convolution have applications in the field of numerical analysis and numerical linear algebra, and in the design and implementation of finite impulse response filters in signal processing. Computing the inverse of the convolution operation is known as deconvolution. == Definition == The convolution of f {\displaystyle f} and g {\displaystyle g} is written f ∗ g {\displaystyle fg} , denoting the operator with the symbol ∗ {\displaystyle } . It is defined as the integral of the product of the two functions after one is reflected about the y-axis and shifted. As such, it is a particular kind of integral transform: ( f ∗ g ) ( t ) := ∫ − ∞ ∞ f ( τ ) g ( t − τ ) d τ . {\displaystyle (fg)(t):=\int _{-\infty }^{\infty }f(\tau )g(t-\tau )\,d\tau .} An equivalent definition is (see commutativity): ( f ∗ g ) ( t ) := ∫ − ∞ ∞ f ( t − τ ) g ( τ ) d τ . {\displaystyle (fg)(t):=\int _{-\infty }^{\infty }f(t-\tau )g(\tau )\,d\tau .} While the symbol t {\displaystyle t} is used above, it need not represent the time domain. At each t {\displaystyle t} , the convolution formula can be described as the area under the function f ( τ ) {\displaystyle f(\tau )} weighted by the function g ( − τ ) {\displaystyle g(-\tau )} shifted by the amount t {\displaystyle t} . As t {\displaystyle t} changes, the weighting function g ( t − τ ) {\displaystyle g(t-\tau )} emphasizes different parts of the input function f ( τ ) {\displaystyle f(\tau )} ; If t {\displaystyle t} is a positive value, then g ( t − τ ) {\displaystyle g(t-\tau )} is equal to g ( − τ ) {\displaystyle g(-\tau )} that slides or is shifted along the τ {\displaystyle \tau } -axis toward the right (toward + ∞ {\displaystyle +\infty } ) by the amount of t {\displaystyle t} , while if t {\displaystyle t} is a negative value, then g ( t − τ ) {\displaystyle g(t-\tau )} is equal to g ( − τ ) {\displaystyle g(-\tau )} that slides or is shifted toward the left (toward − ∞ {\displaystyle -\infty } ) by the amount of | t | {\displaystyle |t|} . For functions f {\displaystyle f} , g {\displaystyle g} supported on only [ 0 , ∞ ) {\displaystyle [0,\infty )} (i.e., zero for negative arguments), the integration limits can be truncated, resulting in: ( f ∗ g ) ( t ) = ∫ 0 t f ( τ ) g ( t − τ ) d τ for f , g : [ 0 , ∞ ) → R . {\displaystyle (fg)(t)=\int _{0}^{t}f(\tau )g(t-\tau )\,d\tau \quad \ {\text{for }}f,g:[0,\infty )\to \mathbb {R} .} For the multi-dimensional formulation of convolution, see domain of definition (below). === Notation === A common engineering notational convention is: f ( t ) ∗ g ( t ) := ∫ − ∞ ∞ f ( τ ) g ( t − τ ) d τ ⏟ ( f ∗ g ) ( t ) , {\displaystyle f(t)g(t)\mathrel {:=} \underbrace {\int _{-\infty }^{\infty }f(\tau )g(t-\tau )\,d\tau } _{(fg)(t)},} which has to be interpreted carefully to avoid confusion. For instance, f ( t ) ∗ g ( t − t 0 ) {\displaystyle f(t)g(t-t_{0})} is equivalent to ( f ∗ g ) ( t − t 0 ) {\displaystyle (fg)(t-t_{0})} , but f ( t − t 0 ) ∗ g ( t − t 0 ) {\displaystyle f(t-t_{0})g(t-t_{0})} is in fact equivalent to ( f ∗ g ) ( t − 2 t 0 ) {\displaystyle (fg)(t-2t_{0})} . === Relations with other transforms === Given two functions f ( t ) {\displaystyle f(t)} and g ( t ) {\displaystyle g(t)} with bilateral Laplace transforms (two-sided Laplace transform) F ( s ) = ∫ − ∞ ∞ e − s u f ( u ) d u {\displaystyle F(s)=\int _{-\infty }^{\infty }e^{-su}\ f(u)\ {\text{d}}u} and G ( s ) = ∫ − ∞ ∞ e − s v g ( v ) d v {\displaystyle G(s)=\int _{-\infty }^{\infty }e^{-sv}\ g(v)\ {\text{d}}v} respectively, the convolution operation ( f ∗ g ) ( t ) {\displaystyle (fg)(t)} can be defined as the inverse Laplace transform of the product of F ( s ) {\displaystyle F(s)} and G ( s ) {\displaystyle G(s)} . More precisely, F ( s ) ⋅ G ( s ) = ∫ − ∞ ∞ e − s u f ( u ) d u ⋅ ∫ − ∞ ∞ e − s v g ( v ) d v = ∫ − ∞ ∞ ∫ − ∞ ∞ e − s ( u + v ) f ( u ) g ( v ) d u d v {\displaystyle {\begin{aligned}F(s)\cdot G(s)&=\int _{-\infty }^{\infty }e^{-su}\ f(u)\ {\text{d}}u\cdot \int _{-\infty }^{\infty }e^{-sv}\ g(v)\ {\text{d}}v\\&=\int _{-\infty }^{\infty }\int _{-\infty }^{\infty }e^{-s(u+v)}\ f(u)\ g(v)\ {\text{d}}u\ {\text{d}}v\end{aligned}}} Let t = u + v {\displaystyle t=u+v} , then F ( s ) ⋅ G ( s ) = ∫ − ∞ ∞ ∫ − ∞ ∞ e − s t f ( u ) g ( t − u ) d u d t = ∫ − ∞ ∞ e − s t ∫ − ∞ ∞ f ( u ) g ( t − u ) d u ⏟ ( f ∗ g ) ( t ) d t = ∫ − ∞ ∞ e − s t ( f ∗ g ) ( t ) d t . {\displaystyle {\begin{aligned}F(s)\cdot G(s)&=\int _{-\infty }^{\infty }\int _{-\infty }^{\infty }e^{-st}\ f(u)\ g(t-u)\ {\text{d}}u\ {\text{d}}t\\&=\int _{-\infty }^{\infty }e^{-st}\underbrace {\int _{-\infty }^{\infty }f(u)\ g(t-u)\ {\text{d}}u} _{(fg)(t)}\ {\text{d}}t\\&=\int _{-\infty }^{\infty }e^{-st}(fg)(t)\ {\text{d}}t.\end{aligned}}} Note that F ( s ) ⋅ G ( s ) {\displaystyle F(s)\cdot G(s)} is the bilateral Laplace transform of ( f ∗ g ) ( t ) {\displaystyle (fg)(t)} . A similar derivation can be done using the unilateral Laplace transform (one-sided Laplace transform). The convolution operation also describes the output (in terms of the input) of an important class of operations known as linear time-invariant (LTI). See LTI system theory for a derivation of convolution as the result of LTI constraints. In terms of the Fourier transforms of the input and output of an LTI operation, no new frequency components are created. The existing ones are only modified (amplitude and/or phase). In other words, the output transform is the pointwise product of the input transform with a third transform (known as a transfer function). See Convolution theorem for a derivation of that property of convolution. Conversely, convolution can be derived as the inverse Fourier transform of the pointwise product of two Fourier transforms. == Visual explanation == == Historical developments == One of the earliest uses of the convolution integral appeared in D'Alembert's derivation of Taylor's theorem in Recherches sur différents points importants du système du monde, published in 1754. Also, an expression of the type: ∫ f ( u ) ⋅ g ( x − u ) d u {\displaystyle \int f(u)\cdot g(x-u)\,du} is used by Sylvestre François Lacroix on page 505 of his book entitled Treatise on differences and series, which is the last of 3 volumes of the encyclopedic series: Traité du calcul différentiel et du calcul intégral, Chez Courcier, Paris, 1797–1800. Soon thereafter, convolution operations appear in the works of Pierre Simon Laplace, Jean-Baptiste Joseph Fourier, Siméon Denis Poisson, and others. The term itself did not come into wide use until the 1950s or 1960s. Prior to that it was sometimes known as Faltung (which means folding in German), composition product, superposition integral, and Carson's integral. Yet it appears as early as 1903, though the definition is rather unfamiliar in older uses. The operation: ∫ 0 t φ ( s ) ψ ( t − s ) d s , 0 ≤ t < ∞ , {\displaystyle \int _{0}^{t}\varphi (s)\psi (t-s)\,ds,\quad 0\leq t<\infty ,} is a particular case of composition products considered by the Italian mathematician Vito Volterra in 1913. == Circular c
PhyCV
PhyCV is the first computer vision library which utilizes algorithms directly derived from the equations of physics governing physical phenomena. The algorithms appearing in the first release emulate the propagation of light through a physical medium with natural and engineered diffractive properties followed by coherent detection. Unlike traditional algorithms that are a sequence of hand-crafted empirical rules, physics-inspired algorithms leverage physical laws of nature as blueprints. In addition, these algorithms can, in principle, be implemented in real physical devices for fast and efficient computation in the form of analog computing. Currently PhyCV has three algorithms, Phase-Stretch Transform (PST) and Phase-Stretch Adaptive Gradient-Field Extractor (PAGE), and Vision Enhancement via Virtual diffraction and coherent Detection (VEViD). All algorithms have CPU and GPU versions. PhyCV is now available on GitHub and can be installed from pip. == History == Algorithms in PhyCV are inspired by the physics of the photonic time stretch (a hardware technique for ultrafast and single-shot data acquisition). PST is an edge detection algorithm that was open-sourced in 2016 and has 800+ stars and 200+ forks on GitHub. PAGE is a directional edge detection algorithm that was open-sourced in February, 2022. PhyCV was originally developed and open-sourced by Jalali-Lab @ UCLA in May 2022. In the initial release of PhyCV, the original open-sourced code of PST and PAGE is significantly refactored and improved to be modular, more efficient, GPU-accelerated and object-oriented. VEViD is a low-light and color enhancement algorithm that was added to PhyCV in November 2022. == Background == === Phase-Stretch Transform (PST) === Phase-Stretch Transform (PST) is a computationally efficient edge and texture detection algorithm with exceptional performance in visually impaired images. The algorithm transforms the image by emulating propagation of light through a device with engineered diffractive property followed by coherent detection. It has been applied in improving the resolution of MRI image, extracting blood vessels in retina images, dolphin identification, and waste water treatment, single molecule biological imaging, and classification of UAV using micro Doppler imaging. === Phase-Stretch Adaptive Gradient-Field Extractor (PAGE) === Phase-Stretch Adaptive Gradient-Field Extractor (PAGE) is a physics-inspired algorithm for detecting edges and their orientations in digital images at various scales. The algorithm is based on the diffraction equations of optics. Metaphorically speaking, PAGE emulates the physics of birefringent (orientation-dependent) diffractive propagation through a physical device with a specific diffractive structure. The propagation converts a real-valued image into a complex function. Related information is contained in the real and imaginary components of the output. The output represents the phase of the complex function. === Vision Enhancement via Virtual diffraction and coherent Detection (VEViD) === Vision Enhancement via Virtual diffraction and coherent Detection (VEViD) an efficient and interpretable low-light and color enhancement algorithm that reimagines a digital image as a spatially varying metaphoric light field and then subjects the field to the physical processes akin to diffraction and coherent detection. The term “Virtual” captures the deviation from the physical world. The light field is pixelated and the propagation imparts a phase with an arbitrary dependence on frequency which can be different from the quadratic behavior of physical diffraction. VEViD can be further accelerated through mathematical approximations that reduce the computation time without appreciable sacrifice in image quality. A closed-form approximation for VEViD which we call VEViD-lite can achieve up to 200 FPS for 4K video enhancement. == PhyCV on the Edge == Featuring low-dimensionality and high-efficiency, PhyCV is ideal for edge computing applications. In this section, we demonstrate running PhyCV on NVIDIA Jetson Nano in real-time. === NVIDIA Jetson Nano Developer Kit === NVIDIA Jetson Nano Developer Kit is a small- sized and power-efficient platform for edge computing applications. It is equipped with an NVIDIA Maxwell architecture GPU with 128 CUDA cores, a quad-core ARM Cortex-A57 CPU, 4GB 64-bit LPDDR4 RAM, and supports video encoding and decoding up to 4K resolution. Jetson Nano also offers a variety of interfaces for connectivity and expansion, making it ideal for a wide range of AI and IoT applications. In our setup, we connect a USB camera to the Jetson Nano to acquire videos and demonstrate using PhyCV to process the videos in real-time. === Real-time PhyCV on Jetson Nano === We use the Jetson Nano (4GB) with NVIDIA JetPack SDK version 4.6.1, which comes with pre- installed Python 3.6, CUDA 10.2, and OpenCV 4.1.1. We further install PyTorch 1.10 to enable the GPU accelerated PhyCV. We demonstrate the results and metrics of running PhyCV on Jetson Nano in real-time for edge detection and low-light enhancement tasks. For 480p videos, both operations achieve beyond 38 FPS, which is sufficient for most cameras that capture videos at 30 FPS. For 720p videos, PhyCV low-light enhancement can operate at 24 FPS and PhyCV edge detection can operate at 17 FPS. == Highlights == === Modular Code Architecture === The code in PhyCV has a modular design which faithfully follows the physical process from which the algorithm was originated. Both PST and PAGE modules in the PhyCV library emulate the propagation of the input signal (original digital image) through a device with engineered diffractive property followed by coherent (phase) detection. The dispersive propagation applies a phase kernel to the frequency domain of the original image. This process has three steps in general, loading the image, initializing the kernel and applying the kernel. In the implementation of PhyCV, each algorithm is represented as a class in Python and each class has methods that simulate the steps described above. The modular code architecture follows the physics behind the algorithm. Please refer to the source code on GitHub for more details. === GPU Acceleration === PhyCV supports GPU acceleration. The GPU versions of PST and PAGE are built on PyTorch accelerated by the CUDA toolkit. The acceleration is beneficial for applying the algorithms in real-time image video processing and other deep learning tasks. The running time per frame of PhyCV algorithms on CPU (Intel i9-9900K) and GPU (NVIDIA TITAN RTX) for videos at different resolutions are shown below. Note that the PhyCV low-light enhancement operates in the HSV color space, so the running time also includes RGB to HSV conversion. However, for all running times using GPUs, we ignore the time of moving data from CPUs to GPUs and count the algorithm operation time only. == Installation and Examples == Please refer to the GitHub README file for a detailed technical documentation. == Current Limitations == === I/O (Input/Output) Bottleneck for Real-time Video Processing === When dealing with real-time video streams from cameras, the frames are captured and buffered in CPU and have to be moved to GPU to run the GPU-accelerated PhyCV algorithms. This process is time-consuming and it is a common bottleneck for real-time video-processing algorithms. === Lack of Parameter Adaptivity for Different Images === Currently, the parameters of PhyCV algorithms have to be manually tuned for different images. Although a set of pre-selected parameters work relatively well for a wide range of images, the lack of parameter adaptivity for different images remains a limitation for now.