Source Code Collection for Reproducible Research

【 http://www.csee.wvu.edu/~xinl/source.html】

“It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong” - Richard Feynman

?

"As a method for finding things out, science lives by its disdain for authority and its reliance on experimentation." - Chris Quigg

?

Welcome on this site about reproducible research in computational science (including signal processing, computer vision, machine learning and neural computation). This site is intended to share the source codes of the latest advances in various technical fields to the best of my knowledge. Only through?Reproducible Research (RR), can we live up to the standard that hard-core science has established since Bacon and Newton. If you know of any release of the source codes that is missing from the list or any broken link, please kindly let me know.

Image denoising

• Wavelet-based soft/hard thresholding and TI denoising??Wavelab
• Spatially adaptive image denoising under overcomplete expansion???SA-OE
• Low-complexity image denoising based on statistical modeling of wavelet coefficientscode
• Bayesian Least-Square Gaussian Scalar Mixture??BLS-GSM
• Wavelet-domain HMM for image denoising??WHMT
• Fields of experts model for image denoising?FoE
• Learning sparse representation for image denoising?K-SVD
• Shape adaptive DCT based image denoising?SA-DCT
• Nonlocal mean based image denoising?codecode2
• Block matching 3D (BM3D) image denoising?BM3D
• Product of Edgeperts denoising??PoEdges
• Total Least-Square (TLS) image denoising?TLS
• AVMF color image denoising??AVMF
• Multiscle LMMSE-based image denoising???code
• Kernel regression based image denoising?code
• Belief propagation for image restoration?code
• Gaussian Field-of-Expert (GFoE) denoising?code
• Active random field learning?code

• Clustering-based Denoising using Locally Learned Dictionaries (K-LLD)

• Local Pixel Grouping (LPG)-PCA image denoising
• Learning Non-Local Range Markov Random Field for Image Restoration?code
• Image denoising via dictionary learning and structural clustering

Image coding

• JPEG-LS standardLOCO-I
• Context-Based, Adaptive, Lossless Image Coding??CALIC
• Edge directed prediction for lossless image compression??EDP
• TMW lossless image compression?Download Code(lost in cyberspace)
• Minimum rate prediction with DP-based optimization??Code
• Embedded Predictive Wavelet Image Coder?Code
• SPIHT image codec??SPIHTMATLAB codes?(third-party implementation)
• Estimation Quantization lossy image codec?EQ
• Least-Square Estionation Quantization CodecLS-EQ
• EBCOT codec for JPEG2000??EBCOT

Image demosaicing

• Primary-consistent soft-decision (PCSD)-based scheme?executable
• Alternate projection (AP)-based scheme?AP
• Adaptive Homogeneity-Directed (AHD) demosaicing??AHD
• DLMMSE demosaicing???DLMMSE
• Demosaicing by successive approximation??SA
• Demosaicing by directional filtering and a posteriori decision??dfapd
• LPA-ICI demosaicing?LPA-ICI
• Lukac's demosaicing toolbox??Download
• A Model of Retinal Local Adaptation for the Tone Mapping of Color Filter Array Images

Image interpolation and Superresolution

• Linear interpolation revitalized
• New edge directed interpolation (NEDI)?code
• Directional filtering and data fusion??DFDF
• Wavelet-based texture image interpolation?wt_interp
• Fast and robust superresolution (SR) toolbox??UCSC-SR
• Superresolution for synthetic zooming?syn_zoom
• EPFL's frequency-domain approach??EPFL
• Support vector machine based image superresolution???result
• Image interpolation using multiscale geometric representations??Code
• Kriging-based Best Linear Unbiased Estimator???Code
• Image interpolation by adaptive 2D autoregressive modeling and soft-decision estimation???Executable
• Super-resolution GUI developed by Bahadir at LSU
• Super-resolution via sparse coding??code
• Super-resolution with sparse mixing estimators
• Machine learning in multi-frame SR
• Example-based learning for super-resolution
• Super Resolution using Edge Prior and Single Image Detail Synthesis?code
• Binary halftone image resolution increasing by decision tree learning
• Simultaneous motion deblurring and super-resolution

Image segmentation/parsing and matting

• Image segmentation by normalized cut??Ncut
• Epitome-based image segmentation??epitome
• Bayesian multiscale image segmentation?SMAP
• Graph-cut Based Image Segmentation??segment
• EDISON System??EDISON
• Pfinder system??Pfinder
• A closed form solution to image matting?matting
• Spectral matting??code
• Level set evolution without reinitialization??Code
• Implicit active contour driven by local binary fitting energy??Code
• Snakes, Shapes, and Gradient Vector Flow?Code
• Unsupervised learning of finite mixture model??Code
• DDMCMC Image Segmentation
• Image Segmentation by Generalized SW-cuts
• A generalized model for scratch detection
• Biased normalized cut
• Global contrast based salient region detection
• Generalizing Swendsen-Wang to sampling arbitrary posterior probabilities?code

Stereo matching& SfM

• A taxonomy and evaluation of dense two-frame stereo correspondence algorithms?code
• Graph cut based stereo matching????code
• Belief propagation based stereo matchingcode
• A roadmap to the integration of early visual modules??Code
• Adaptive support-weight approach??Code
• Energy minization based stereo matching
• Energy Based Multiple Model Fitting for Non-Rigid Structure from Motion?code

Image deblurring

• Fourier-Wavelet Regularized Deconvolution?ForWard
• Pointwise SA-DCT regularized deconvolution?SA-DCT
• Image deconvolution using a natural image prior??Code
• Total-Variation (TV) based image deblurring?Code
• Two-step iterative shrinkage/thresholding algorithms for image restoration?Code
• Iterative methods for image restoration??Code
• ICA Toolbox for blind image separation
• L0-AbS Deblur 1.0

• Regularized Kernel Regression-Based Deblurring (AKTV)

• Projection-based deblurring with fine-granularity and spatially adaptive regularization
• Fast Gradient-Based Algorithms for Constrained Total Variation Image Deblurringcode
• Image deblurring by adaptive sparse domain selection and adaptive regularization?code

Blind image deblurring

• Removing Camera Shake from a Single Image?code_request_form
• Coded exposure for motion deblurring
• Invertible Motion Blur in Video
• High-quality blind motion deblurring (executables only)
• Quality measure for Blind deblurring methods

• Eficient Marginal Likelihood Optimization in Blind Deconvolution?code

• Analyzing spatially varying blur
• blind deconvolution using a normalized sparsity measure
• Blur Kernel Estimation using the Radon Transform?code

?

Image inpainting/Texture synthesis

• Exemplar-based image inpainting??code
• Fields of experts model for image inpainting??FoE
• Image recovery via adaptive sparse representation?code
• Least-Square based sequential error concealment??nsec
• Patch-based nonlocal error concealment
• Wavelet-domain parametric model??code
• Image recovery via hybrid sparse representation

• Higher Order SVD Analysis for Dynamic Texture Synthesis

PDE-based image processing

• Perona-Malik nonlinear diffusion??code?code2
• Total variation based image denoising?codecode2
• Shock filter for image enhancement???code
• Weickert's anisotropic diffusion??code
• Mean curvature diffusion (MCD)???code
• A variational method for image recovery?code

Image quality assessment

• Universal image quality index???code
• Structural SIMilarity (SSIM) index???code
• Degradation model??code
• FSIM: A Feature Similarity Index for Image Quality Assessment?code

Biometrics

• Fingerprint enhancement and matching
• Daugman's iris recognition algorithm implementation

• Photorealistic Models for Pupil Light Reflex and Iridal Pattern Deformation

• Gabor Feature based Sparse Representation for Face Recognition?code
• Robust Sparse Coding for Face Recognitioncode
• Face recognition software at face-rec.org
• Ling Feng's speaker recognition sources

?

HDR imaging

• HDR image rendering using a retinex-based adaptive filter

• Digital Camera Workflow for HDR Images Using a Model of Retinal Processing

• HDR image rendering by iCAM06 model
• Rafal Mantiuk's research on HDR imaging

Gradient-domain image processing

• Distributed Gradient-Domain Processing of Planar and Spherical Images

• GradientShop:A Gradient-Domain Optimization Framework for Image and Video Filtering

• Local Laplacian Filters: Edge-aware Image Processing with a Laplacian Pyramid

• Domain Transform for Edge-Aware Image and Video Processing

Video coding

• MPEG-1/2 reference software
• H.263/H.263+ reference software
• MPEG4 reference software (MoMuSys version)
• H.264/AVC reference software
• 3D SPIHT video coding?code
• DISCOVER video codec for DVC
• HEVC (H.265) Refence model in development

Texture classification

• Wavelet-based GDD and KL-distance?code
• Local binary pattern (LBP) based
• Filter bank based at Visual Geometry Group
• A Completed Modeling of Local Binary Pattern Operator for Texture Classification?code

Object recognition

• Adaboost method????code
• Biologically inspired object recognition?code
• Hierarchical Models of Object Recognition in Cortex??code
• Scalable recognition with a vocabulary treeCode
• Shock graphscode
• Shape contexts??code
• Robust nonrigid point matching???Code
• Recognizing and learning object categories?(short course at ICCV2005)
• Beyond Bag of features?Code
• SuperParsing?Code
• Aggregating Gradient Distributions into Intensity Orders

?

Blind source separation

• Shiro Ikeda's page of?Blind Source Separation
• Independent Component Analysis by JV Stone
• Blind source separation via Independent component analysis
• Two-microphone Separation of Speech Mixturescode

Image registration

• Affine SIFT (ASIFT) with online demo
• Lukas-Kanade algorithm??code?code2
• SIFT feature correspondence?code?code2?code3
• Local binary pattern (LBP)???code
• Maximally stable extremal regions (MSER)?code
• Graph-cut based??optical flow estimation??code
• Pyramid-based hierarchical motion estimation??Code
• Affine Motion Estimation for Medical Image Registration??Code
• A frequency-domain approach toward image registration??Code
• Blended Intrinsic Maps

Visual tracking

• Object detection and tracking in motion sequence
• Incremental Learning for Robust Visual Tracking?code
• Online Visual Tracking with Histograms and Articulating Blocks?code

• Kanade-Lucas-Tomasi Feature Tracker

• SIFT keypoint detector?code2?code3
• Speeded-Up Robust Features (SURF)
• Histogram of oriented gradients (HOG) based human detection
• Visual tracking using appearance model and particle filters?(plug-in to opencv)
• Video Object Segmentation by Tracking Regions?code

?

Manifold learning and embedding

• A Global Geometric Framework for Nonlinear Dimensionality Reduction????code
• Nonlinear Dimensionality Reduction by Locally Linear Embedding???code
• Laplacian Eigenmaps??code
• Diffusion maps?code
• Manifold learning toolbox&demo

Wavelets and frames

• A Wavelet Tour of Signal Processing??Wavelab
• Steerable PyramidmatlabPyrtools.tar.gz
• Rice Wavelet Toolbox?rwt.zip
• Contourlet and Ridgelet Toolbox????download
• Beamlet and Curvelet Toolbox????Beamlab
• Complex wavelet Toolbox????download
• Wavelet/bandelet Toolbox at Matlab Central
• MCALab
• Differentiation of discrete multidimensional signals?code

Compressed Sensing

• l1-Magic
• SparseLab
• GPSR
• ell-1 LS: Simple Matlab Solver for ell-1-Regularized Least Squares Problems
• sparsify
• MPTK: Matching Pursuit Toolkit?[See also related conference publication:?ICASSP 2006]
• Bayesian Compressive Sensing
• SPGL1: A solver for large scale sparse reconstruction
• sparseMRI
• FPC
• CVX
• Chaining Pursuit
• Regularized OMP
• SPARCO: A toolbox for testing sparse reconstruction algorithms?[See also relatedtechnical report?]
• TwIST
• Compressed Sensing Codes
• Fast CS using SRM
• FPC_AS
• Fast Bayesian Matching Pursuit (FBMP)
• SL0
• Sparse recovery using sparse matrices
• PPPA
• Compressive sensing via belief propagation
• SpaRSA
• KF-CS: Kalman Filtered CS (and other sequential CS algorithms)
• Fast Bayesian CS with Laplace Priors
• YALL1
• TVAL3
• RecPF
• Basis Pursuit DeQuantization (BPDQ)
• k-t FOCUSS
• Sub-Nyquist sampling: The Modulated Wideband Converter
• Threshold-ISD
• A Sparse Learning Package
• Model-based Compressive Sensing Toolbox
• Sparse Modeling Software
• Spectral Compressive Sensing Toolbox
• CS-CHEST: A MATLAB Toolbox for Compressive Channel Estimation
• DictLearn: A MATLAB Implementation for Dictionary Learning
• SPAMS
• Peformance benchmark of l1-optimization algorithms
• BM3D-based compressed sensing

Evolutionary computing

• Ant colony optimization
• Genetic algorithm toolbox
• Particle Swarm Optimization Toolbox

Networking Research

• The network simulator (ns-2)
• NetSim at Tetcos
• LBNL's software releases

Biomedical Imaging

• SparseMRI Toolbox
• Image reconstruction toolbox
• medical image registration
• Level set based medical image segmentation
• Gradient vector flow
• Compressed sensing image reconstruction via recursive spatially adaptive filtering
• multiresolution celluar image classification
• multirate fluorescence microscopy image acquisition

Data Clustering

• Unsupervised learning of finite mixture models?code
• Affinity propagation
• On Spectral Clustering: Analysis and an algorithm?code?code2?code3
• Nonnegative matrix factorization (NMF)?code2code3
• Fast kmeans via triangle inequality
• kdtree-based NN/kNN search?fast kNN searchcode2
• RANSAC toolbox for robust fitting
• Clustering Through Ranking On Manifolds?code

Sampling&Simulation

• Poisson-disk sampling

• Filtering solid Gabor noise

?

Graphics, Cartoons&Motion

• Apparent Layer Operations for the Manipulation of Deformable Objects

• 2.5D cartoon models
• 3D modeling with sihouettes

• Real-time Large-deformation Substructuring

• Generalized biped walking control
• Locomotion Skills for Simulated Quadrupeds
• Action Recognition from a Distributed Representation of Pose and Appearance

?

Machine learning&Neural Networks

• Deep Boltzmann Machines
• Support vector machine
• SVM and kernel method toolbox
• Object detection with Boosting
• Convolutional/Deconvolutional networks
• Hopfield networks?code
• Self-organizing map (SOM) Toolbox
• Reservoir Computing Toolbox
• Polychronization: Computation With Spikes
• Slowly coupled oscillators: phase dynamics and sync
• Liquid State Machines(LSM)?code
• Echo state networks for harnessing nonlinearity?code
• Image segmentation by LEGION network?code

Miscellaneous

• Simple model of spiking neurons?spike train analysis
• Direct LS-based ellipsis fitting??code
• Graph cut based 2D Phase unwrapping???code
• DACE: a MATLAB Kriging toolbox
• Inference package for undirected graphical models
• Kernel smoothing toolbox
• CMU statistics library collections
• Complex network toolbox
• DistLearnKit: a MATLAB Toolkit for distance metric learning
• Subspace segmentation source code distribution
• Multiview geometry and 3D reconstruction
• A probabilistic image jigsaw puzzle solver

Links to other communities' reproducible research effort

• Geostatistics toolbox?mgstat?DACE
• Error Correcting Codes (ECC)
• Computer graphics?graphics papers on the web
• Computer vision?CV papers on the web
• Machine learning
• DMOZ Open Directory Project
• MATLAB toolbox collection at Plymouth
• Neurophysiological data analysis

Links to reproducible books/journals/tutorials

• Image Processing Online (IPOL)
• Gradient Domain Manipulation Techniques in Vision and Graphics

• Statistical and Structural Recognition of Human Actions

• Distance functions and metric learning
• Feature Learning for Image Classification
• Recognizing and Learning Object Categories

• Physics-Based Human Motion Modelling for People Tracking

• 3d Shape Reconstruction from Photographs: a Multi-View Stereo Approach

• Deblurring Images: Matrices, Spectra, and Filtering
• Natural image statistics
• Spikes, decisions & actions
• Multiple view geometry in computer vision
• Collective Animal Behavior
• Signal Processing Techniques for Spike Train Analysis using MatLab

Links to other individual's reproducible research

• Adrian Barbu's research codes release
• Al Hero's Lab and his reproducible research
• Amir Beck's work on optimization theory and applications
• Amir Saffari's?reproducible?reseach code releases
• Amit Agrawal's Matlab and C codes
• Anand Rangarajan 's matlab codes on hisreproducible?research
• Anat Levin's matlab codes release
• Andrew Davison's work on Computational neuroscience
• Ann Lee's Diffusion maps and treelet
• Andrew Zisserman's visual geometry group source codes
• Antonio Torralba's research codes release
• Ashok Veeraraghavan's?reproducible?research code release

• Ayan Chakrabarti's?reproducible?research code release

• Bill Freeman's software release on his group's?reproducible?research
• Bob Kass' research codes on neuronal data analysis
• Ce Liu's software release on hisreproducible?research
• Christopher Kanan's?reproducible?research code release
• Chuck Anderson's matlab codes on NNs and reinforcement learning
• Dan Ellis' MATLAB Audio Processing Examples
• David Heeger's toolboxes
• Deliang Wang's research codes release
• Deqing Sun's?reproducible?research code release
• Deva Ramanan's work on object recognition
• Eugene M. Izhikevich's matlab codes on NNs
• Guy Gilboa's matlab codes on PDE-based image processing
• Leo Grady's Graph Analysis Toolbox for Image Processing
• Jalal Fadili's source codes on sparse representation
• Jelena Kovacevic: bimagicLab: Software
• Jeffrey A. Fessler's matlab codes release
• Jian Sun's research code release
• JianChao Yang's source codes on image classification and super-resolution
• Jiaya Jia's programs and executables
• Jon Wellner's work on statistics
• Julien Mairal's matlab toolbox for sparse coding and dictionary learning
• Kai Yu's?reproducible?research codes release
• Kevin Murphy's Bayes Net Toolbox for Matlab
• Laurens van der Maaten's software collection
• Laurent Perrinet's SparseHebbianlearning source codes
• LCAV's reproducible research at EPFL
• LEAR's learning and recognition in vision
• Lei Zhang's MATLAB codes releases
• Leo Grady's matlab codes on his?reproducibleresearch
• Malcolm A. MacIver's AnimalLab
• Marco Zuliani's?reproducible?research codes release
• Mariana S. C. Almeida 's?reproducibleresearch code release
• Mark Schmidt's reseach on learning on probabilistic graphical models
• Matthew Zeiler's?reproducible?research code release
• MD Anderson Cancer Center: Bioinformatics
• Michael Elad's source code collection on his research
• Micheal Jordan's research code release
• Ming-ming Chen's?reproducible?research code release
• Ming-Hsuan Yang's?reproducible?research works
• Neil Lawrence's reproducible research in machine learning
• Onur Guleryuz's research codes release
• Patrik O Hoyer's source code collection on his?reproducible?research
• Peter Getreuer's?reproducible?research code release
• Peyman Milanfar's source code collection on his?reproducible?research
• Rene Vidal's Visionlab?reproducible?research code release
• Raj Gupta's?reproducible?research code release
• Rick Chartland's release on his?reproducibleresearch
• Shaoting Zhang's?reproducible?research code release
• Simoncelli's LCV?reproducible?research codes release
• Sinisa Todorovic's?reproducible?research codes release
• Song-chun Zhu's source codes on image segmentation and active basis
• Tony Xu Han's?reproducible?research code release
• UCF vision lab source code collection
• UIUC's salient patch feature collection
• USC's iLab Neuromorphic Vision C++ Toolkit
• UWO vision lab?reproducible?research code release
• Vanderbilt's StatReport
• Wotao Yin's research code release
• Xavier Bresson's source codes accompanying his papers on image processing
• Xiaofei He's dimensionality reduction source code collection
• Xubo Song's matlab codes on her?reproducibleresearch
• Yi Ma's source code collection on hisreproducible?research
• Yu-wing Tai's?reproducible?research code releases
• Yue M Lu's source codes on his?reproducibleresearch

???Google Scholar?is great but if most papers in computational sciences could be accessed along with their source codes (not just the citation number), the world for scientific researchers will be even better. It is easy to find papers these days but when can finding the?source codes of a paper become easy too? I think Don Knuth's old-day advices on?Literate Programming?are still relevant to the current state of reproducible research. I believe that the time is ripe for significantly promoting experimentally reproducible research (just like mathemathetical theories - mentally reproducible research), and that we can best achieve this by considering research codes to be works of literature (so they can be easily picked up by other researchers). Only when the reproducibility of research in computational science becomes a default instead of a luxury, can we look further by standing on each other's shoulders.

一個好的資源整合網址：

http://www.csee.wvu.edu/~xinl/source.html

總結

以上是生活随笔為你收集整理的Source Code Collection for Reproducible Research的全部內容，希望文章能夠幫你解決所遇到的問題。

如果覺得生活随笔網站內容還不錯，歡迎將生活随笔推薦給好友。