Source Code Collection for Reproducible Research

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.

一个好的资源整合网址：

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