sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
22e76729fe1ea0f80512eba4fb5cf812e3cfc43ffe0a5370a229c8c9ada21138 | MATLAB | 953 | 34 | function [P,T,L,r,centerX,cX]=kernelEVD(X);
%KERNELEVD (kernel eigenvalue decomposition) performs a singular value decomposition
% of a matrix with more columns than rows.
%
% Required input:
% x : data matrix of size n by p where n < p (else classSVD is invoked)
%
% I/O: [P,T,L,r,centerX,cX]=kernelEVD(X);
%
% T... |
26dc552661d8e8a33e66098f1945bed66e6e9427a966f696c51808defee4114f | MATLAB | 955 | 39 | % NDMwS
%
% Evaluate NDMwMC predictions [y] at desired time stamps.
%
% Input:
% x0 = Initial Condition
% time_stamps = provided in units given by experiment
% C = connectivity matrix
% beta = diffusivity parameter
% alpha0 = cte growth/decay term dependin... |
7353bc6d061d5026af9a859f8aed886364307bfa41fadfea181bcff7c30ba3af | MATLAB | 955 | 34 | function draw_signifpatch(time,sign_p,col)
%DRAW_SIGNIFPATCH
% DRAW_SIGNIFPATCH(time,sign_p,col) draws a filled rectangle with reduced opacity
% where significant differences were detected across time.
% Input parameters:
% TIME time vector of plotted figure
%
% SIGN_P significance vector of 0s and 1s... |
f030860cd1470afcc8cd74344f783279f08256487579669b2114424e3479518a | MATLAB | 955 | 26 | function [ nexFile ] = nexAddEvent( nexFile, timestamps, name )
% [nexFile] = nexAddEvent( nexFile, timestamps, name ) -- adds an event
% (series of timestamps) to nexFile data structure
%
% INPUT:
% nexFile - nex file data structure created in nexCreateFileData
% timestamps - vector of event timestamp... |
fc8eb7632698e19f8bbf89feae66a98258340931e261bc70f9b26cf2ee3ef3a8 | MATLAB | 955 | 45 | function V = solveV_eig(U, Us, Vs, Ss, reg_smooth, reg_l2)
% solve S analytically using eigen-decomposition
%
% TODO: check with optimization form.
n = length(Ss);
UtU = U' * U;
[Q1, Lu] = eig(UtU);
V = cell(n, 1);
for ii = 1:n
V{ii} = solveVi(U, Us, Q1,... |
417bbb1129b939a5856f94a0bc8cd999660aab33d48a7db34c4bc94c8f196da3 | MATLAB | 957 | 33 | function cmap = green_white_magenta(n)
%GREEN_WHITE_MAGENTA Creates a green-to-white-to-magenta colormap
% usage example:
% colormap(green_white_magenta(256));
% colorbar;
%
% cmap = GREEN_WHITE_MAGENTA(n) returns an n-by-3 colormap array.
% If n is not specified, it defaults to 256.
if nargin < 1
n = ... |
1867c1db0bf845b3d6e4d3e480ecb1a05a674d40f61445a74d5de0b9c3cf2c6f | MATLAB | 959 | 39 | function entry = findindict(c,dcode)
% Look up an entry in the dictionary
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
% $Id: findindict.m 7147 2017-08-03 14:07:01Z spm $
entry = [];
d = getdict;
d = d.(dcode);
if ischa... |
8bb6b500576d269240da6a120fc69d174e6d17e05e8c6c85634a1c5f2ebf8957 | MATLAB | 960 | 25 | matdir = '/Users/justintorok/Documents/MATLAB/Nexis/raw_data_mouse';
load([matdir filesep 'eNDM_mousedata.mat'],'Networks');
load([matdir filesep 'KaufmanDiamond_datasets_dat&seed.mat']);
load([matdir filesep 'regional_Gene_Data.mat'],'regvgene_mean');
C = Networks.ret/max(Networks.ret(:));
tpts = tpts.DS6;
data = data... |
e218d4f765f48e477efdf7bc24f773d447a2bad0f0176751cfe524767e4b8bdf | MATLAB | 963 | 29 | <<<<<<< HEAD
function tf = isfield(this,field)
% Isfield method for GIfTI objects
% FORMAT tf = isfield(this,field)
% this - GIfTI object
% field - string of cell array
% tf - logical array
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust C... |
c3ddd71b31b3ddb339a822e3052f0ff26260e231e009f2ebe41efab6a6ee0ab0 | MATLAB | 965 | 31 | function P = nk_CreateSVMParamArray(Param, P)
P.SVM = Param;
ctype = nk_GetLIBSVMClassType(P.SVM);
switch ctype
case {0,4}
P.Params{1} = Param.SlackParam;
P.Params_desc = {'SlackParam'};
case 1
P.Params{1} ... |
e3875f806cc9ed599786ce1fb306c6799b5986eb00267ff9d729119826d3110c | MATLAB | 968 | 34 | function IsoDist = IsolationDistance(FD, ClusterSpikes)
% IsoDist = IsolationDistance(FD, ClusterSpikes)
%
% Isolation Distance
% Measure of cluster quality
%
% Inputs: FD: N by D array of feature vectors (N spikes, D dimensional feature space)
% ClusterSpikes: Index into FD which lists spikes fr... |
394d005ac1cb8e28ab09ac4a1c36ce56385fc6d29c2bc4c566899303096a9769 | MATLAB | 969 | 25 | clear
%% graphing of response delays to show distribution
load('ProcessedData\PreProcessed_50window.mat');
Pre_delays_pull = cell2mat(horzcat(Pre_Delay_byDay{1,:}));
delays_pull = cell2mat(horzcat(Delay_byDay{1,:}));
% drop blanks
delays_pull(delays_pull == 0) = [];
Pre_delays_pull(Pre_delays_pull == 0) = [];
%... |
94e40ef356f610f70ff56665d86c9cea020b152a87c81267772efe670995e01c | MATLAB | 969 | 33 | function e=num2cellstr(m)
% numerical matrix to cell str of the same size
%%%%
% Copyright (C) <2012> <Yifeng Li>
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the Lice... |
1ab22a87c3d7651a49ad3ff0487db05b88470d4f8c71308eb5d4962363e854a7 | MATLAB | 970 | 36 | function spmTest
%this loads sample overlays
% each overlay has two contrasts/timepoints
% examples saved in both GIfTI and MZ3 format
%load GIfTI
fnm = fullfile(spm('Dir'),'canonical','cortex_5124.surf.gii');
if ~exist(fnm,'file')
error('Unable to find file (it comes with spm12): %s', fnm);
end
tic;
g = gifti(fn... |
22b0b821bdc7d0bdc5afb3784f442678a918da81a933322e82dcdf24ed7b6a96 | MATLAB | 971 | 34 | function [eigNormalized, varargout] = mbm_normalize_eig(eig, nEig, varargin)
% normalise each column of eig by dividing by its norm.
%
%% Inputs:
% eig - Matrix of columns of eigenmodes.
%
% nEig - Number of eigenmodes.
%
%% Output:
% eigNormalized - Matrix of columns of normalized eigenmodes.
% Trang Cao, ... |
762337c2d0a5a4365ed4d32a4e2a4c7835068369f1c197458f4ec7164ae3be32 | MATLAB | 972 | 27 | %SPARSE_NN
%
% This file is part of the Matlab Toolbox for Dimensionality Reduction.
% The toolbox can be obtained from http://homepage.tudelft.nl/19j49
% You are free to use, change, or redistribute this code in any way you
% want for non-commercial purposes. However, it is appreciated if you
% maintain the name of ... |
814a12ac78a58301176845437f860c77c8251bb04586a8b0b13eb812defbe3f9 | MATLAB | 973 | 26 | function mappedX = run_data_through_network(network, X)
%RUN_DATA_THROUGH_NETWORK Run data through the network
%
% mappedX = run_data_through_network(network, X)
%
% Runs the dataset X through the parametric t-SNE embedding defined in
% network. The result is returned in mappedX.
%
% This file is part of the Matlab ... |
e0e7be7848bd774514b2886d5f72b5286922aca968c59e8e806983bb2edcd0ea | MATLAB | 975 | 31 | function Q = M2Q(M)
% Convert from rotation matrix to quaternion form
% See: http://skal.planet-d.net/demo/matrixfaq.htm
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
% $Id: M2Q.m 7147 2017-08-03 14:07:01Z spm $
d = diag... |
e403dee58f9e762f7bbc3150f1be5c58356c1b31f200fd44c56c6ec1e33597de | MATLAB | 980 | 37 | rootfolder = 'Z:\data\EXP\';
%%
compile_spontdbs;
%%
for j = 1
if ~isempty(db(j).expts)
moviefolder = fullfile(rootfolder, db(j).mouse_name, db(j).date,...
num2str(db(j).expts(1)));
else
moviefolder = fullfile(rootfolder, db(j).mouse_name, db(j).date);
end
% process all sav... |
1acc458f56bf9d344480c9d304f72a0c5a5538cd8168f2db633676bdefb9280a | MATLAB | 981 | 49 | function [H,grad,iter] = nlssubprob(V,W,Hinit,tol,maxiter)
% H, grad: output solution and gradient
% iter: #iterations used
% V, W: constant matrices
% Hinit: initial solution
% tol: stopping tolerance
% maxiter: limit of iterations
%global glbnumt
H = Hinit;
WtV = W'*V;
WtW = W'*W;
alpha = 1; beta = 0.1;
for ite... |
2aaed1d3f27a76200a94505f2ad9dc5a0596a43936651eccbdc62b1ff417a513 | MATLAB | 982 | 41 | function [] = plx_ad_info(filename)
% plx_ad_info(filename): prints .plx file a/d channel info
%
% plx_ad_info(filename)
%
% INPUT:
% filename - .plx file name. Will use file open dialog if filename is empty string
%
% OUTPUT:
% (none)
if nargin ~= 1
error 'expected 1 input argument';
end
[ filename, isPl2 ] ... |
ad229f9b846f32ae8231fecf9c62cb1eb581c325abfb21602e2b92f9c929039e | MATLAB | 982 | 42 | function [MI, alph, optk] = nk_EstimKforMIPerm(Y,Labels,kstart,kend,nperms)
[kX, ix] = size(Y);
kvec = kstart:kend;
kvecX = length(kvec);
miK = zeros(ix,kvecX);
alphK = miK;
meanmiK = zeros(ix,kvecX);
varmiK = zeros(ix,kvecX);
miperm = zeros(nperms,1);
TrainInd = zeros(nperms,kX);
for i=1:nperms
TrainInd(i,:) = r... |
6e23e991edda0d28db9ef73b7b0be96627c2dd05301f399fe0a52573500cafda | MATLAB | 983 | 40 | function nk_make(srcdir)
% =========================================================================
% function nk_make(srcdir)
% -------------------------------------------------------------------------
% Inputs:
% srcdir : source directory of files (<nm root>/cfiles)
% This function compiles all C fi... |
a5c916efe30dd8ed21daf51b6c6355f9db800e483ee867ec2833f6b5c5a478f7 | MATLAB | 985 | 30 | function C=clustering_coef_wu(W)
%CLUSTERING_COEF_WU Clustering coefficient
%
% C = clustering_coef_wu(W);
%
% The weighted clustering coefficient is the average "intensity"
% (geometric mean) of all triangles associated with each node.
%
% Input: W, weighted undirected connection matrix
% ... |
3389b5a0d006de9b7b3fd77f58e11ffe891c95921e3011623d4e1f0ec8a97d46 | MATLAB | 986 | 33 | function f = cal_mi(I1,I2)
% A function with the simplest form to
% compute Mutual Information of two images
% written by HU Xiubing
% Wuhan University,China
% huxb@whu.edu.cn
size1 = size(I1);
size2 = size(I2);
if ne(size1,size2)
error('Please enter the same size images ! ');
end
I1 = I1(:);
I2 = I2(:);
min1 = m... |
445473e4458c4b9163c62b4edc65cbb2b15bb1a1fe7a4efc7f5c2c88741fe39f | MATLAB | 988 | 25 | function p_map = compute_analytical_pvals(labels, X, w_star)
% p_map = compute_analytical_pvals(labels, X, w_star)
% Compute analytical multivariate P values using the formulation of Gaonkar
% et al. "Interpreting support vector machine models for multivariate group
% wise analysis in neuroimaging", Medical Image Analy... |
4aa5fe4d46de59fb04a913fd7b934610a80316f16b43286475d0b421f3927d56 | MATLAB | 989 | 32 | function C=getRelationMatrix(ind)
% ind: logical matrix
% C: numerical matrix
%%%%
% Copyright (C) <2012> <Yifeng Li>
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the ... |
7b03fe89eb426c9ffc6c00e43ff89714dde88e6d31e563c2ee2c4b5c1dbd388b | MATLAB | 990 | 44 | function calcFD_save(fname,fd,subjects,labels,labelfile)
% Output the FD values to a txt file
% 20151024 CRM
%
% 20180503 SK: modified to read in the headers from label file if provided,
% else labels are numerical
%
% file identifier
fid = fopen(fname,'w') ;
% headers
fprintf(fid,'%s\t','subID.calcF... |
67b690da34af7a6ef5e9507370b91eec7ef5fe8fbbe542129f8aebe056084c4e | MATLAB | 993 | 28 | function D = agreement_weighted(CI,Wts)
% AGREEMENT_WEIGHTED Weights agreement matrix
%
% D = AGREEMENT_WEIGHTED(CI,WTS) is identical to AGREEMENT, with the
% exception that each partitions contribution is weighted according to
% the corresponding scalar value stored in the vector WTS. As an example,
% su... |
cfbe4873b158d1bf7bd3c9807e6b95b9f671464e50c63fc1c8e61b0d3d4be9b7 | MATLAB | 994 | 36 | function silhouetteplot(sylinf,n,class)
%SILHOUETTEPLOT creates a silhouetteplot for output of the cluster
% algorithms pam or fanny.
%
% I/O: silhouetteplot(sylinf,n)
%
% This function is part of LIBRA: the Matlab Library for Robust Analysis,
% available at:
% http://wis.kuleuven.be/stat/robust.html
%
... |
1cfb26a845dfd346a4dd56396fd32f88487fe7e7f37ab254afded85a21a9389f | MATLAB | 997 | 35 | function [rmse, rrmse, pcc] = compute_metrics(x_gt, x_hat)
%COMPUTE_METRICS Time-domain metrics between ground truth and reconstruction.
% [rmse, rrmse, pcc] = compute_metrics(x_gt, x_hat)
%
% Inputs:
% x_gt : 1 x T or T x 1 ground-truth signal
% x_hat : 1 x T or T x 1 reconstructed signal
%
% Outputs:
% rmse... |
bb725101a9eafda75b7f160b31121cfcb69ceb59d1946fb7eeb246d0adb7cbc6 | MATLAB | 997 | 46 | function [model] = ml_binaryclass_brokenStump(X,y,options)
% ml_binaryclass_brokenStump(X,y,options)
%
% Description:
% - Finds the best threshold across all features by minimizing the
% number of misclassifications
%
% Options:
% - None
%
% Authors:
% - Mark Schmidt (2014)
[nTrain,nFeatures] = size(X);
... |
5324b7b2297806ec25147f5168ee5a6ef02951985898b5a8ede2ebd16dc63d62 | MATLAB | 1,000 | 34 | function [flow_mat] = FlowCalculator(X_,C_,beta_,isndm,U_,b_)
% This function will calculate the flows between each pair of regions using
% the NDM and eNDM frameworks
%isndm is a binary flag - where replaced by 1 means the model is for the
%standard ndm and if 0 then it means the model is for eNDM
nroi = size(C_,1);... |
a1a0fd32ab0549ba8ddf56b7376358eddd3c2a082cec8448abfda4cc70573ac7 | MATLAB | 1,002 | 29 | function [Thresh, Crit, Mx, YnewPred, YPerf, YnewPerf] = nk_DefineThresh(FEATSEL, Y, DScore, labels, Ynew, labelnew, sigma, curclass)
Mx = []; YnewPred = []; YPerf=[]; YnewPerf=[];
% Determine threshold
switch FEATSEL.salthreshmode
case 0
Thresh = []; Crit = [];
case 1 % Percentile
if numel(FE... |
b0b124cc980a187d4fbf1280d0b4b7a5dafcad1b091155b07e448050bb809846 | MATLAB | 1,002 | 26 | function [Y] = diagonalize(X,samplesize)
% ----------------------- Input ------------------------------
% X: samples of all tasks (each row is a sample)
% samplesize: the i-th entry is the sample size of the i-th task
% ----------------------- Output -----------------------------
% Y: sparse data matrix which is diagon... |
bf548106c09842d9f1c2327c6dbeac1a97edbc46fc1554a8c403b6d4151bc4f9 | MATLAB | 1,002 | 32 | function est = mripy_est_from_PEB(PEB, norm)
% Extract estimates from a PEB object.
% est.A, est.B, est.C, est.PA, est.PB, est.PC
if nargin < 2
norm = false;
end
n_params = size(PEB.Pnames, 1);
for k = 1:n_params
if norm
eval(['est.', PEB.Pnames{k}, ' = ', num2str(full(PEB.... |
765b381702218ce8101e6c4adcded89f609eb38bdaae7e0b9c33b5900fc67dd2 | MATLAB | 1,006 | 42 | function demo()
%
% demonstration file for NMFLibrary.
%
% This file illustrates how to use this library.
% This demonstrates multiplicative updates (MU) algorithm and
% hierarchical alternative least squares (Hierarchical ALS) algorithm.
%
% This file is part of NMFLibrary.
%
% Created by H.Kasai on Apr. 05, 2017
... |
0b708b48f83c5b47ae97cdcafc3e765f3935e52fc76a64bd3045ae8c9311dcfa | MATLAB | 1,007 | 45 | % write face movie to binary file and then load to do SVDs, projections,
% pupil computations
function h = processROIs(h)
%%
tic;
% compute mean from a subset of frames
h = subsampledMean(h);
h.nframes = int64(h.nframes);
%%
% compute svd of videos ----------------------------- %
h = computeSVDmotion(h);
%% pupil, ... |
3e222a53f7c50768906be3124abb6096e077181427315c773d6f0683bf25c2b7 | MATLAB | 1,007 | 29 | function j=JSM(K,trainClass)
% compute the ratio of within class distance to between class distance
% K: kernel matrix
% trainClass: column vector, the class labels
% j: scalar, the ratio
%%%%
% Copyright (C) <2012> <Yifeng Li>
%
% This program is free software: you can redistribute it and/or modify
% it under the t... |
17748fcca586792e81c237e7b3930d3fe7f6a26b7e65bc2682445ed77c2d599d | MATLAB | 1,008 | 36 | function import_coma
os_prefix = './psg_data/';
for j = 1:1
import(os_prefix,'coma',j);
end
for j = 1:1
import(os_prefix,'control_coma',j);
end
function import(os_prefix,data_set,k)
infile = fullfile(os_prefix,data_set,sprintf('%s_%d.mat',data_set,k));
fprintf('Loading: %s\n',infile);
fhandle = load(inf... |
fdd33082acccdb748d3863236116caa4fe7d1be01bba31e4a6670a9db1fd7c69 | MATLAB | 1,013 | 29 | function autoenc = roll_out(network)
%ROLL_OUT Rolls out an autoencoder
%
% network = roll_out(network)
%
% Rolls out a stack of RBMs as an autoencoder that can be finetuned using,
% e.g., backpropagation.
%
% This file is part of the Matlab Toolbox for Dimensionality Reduction.
% The toolbox can be obtained from h... |
249e80f6fffc5f9693ca1c029b89e867359320ee971c11946389528a3028e929 | MATLAB | 1,015 | 33 | function initialise(fa)
% Initialise file on disk
%
% This creates a file on disk with the appropriate size by explicitly
% writing data to prevent a sparse file.
%__________________________________________________________________________
% Copyright (C) 2013-2017 Wellcome Trust Centre for Neuroimaging
%
% $Id: initia... |
7e824159be598bcfff827aabf0ff9c6fabf1a476a273b7f568ef7cc0694c41a3 | MATLAB | 1,016 | 34 | function [Q, R] = mgs(A)
%MGS Performs a modified Gram-Schmidt orthogonalization
%
% [Q, R] = mgs(A)
%
% Performs a modified Gram-Schmidt orthogonalization. This is a more stable
% way to compute the Gram-Schmidt orthogonalization than Matlab's one.
%
%
% This file is part of the Matlab Toolbox for Dimensionality Re... |
7936c5f58d9ea6aafd2dc3e6958e3d07e2987b08245d887cba6badf038e9dce4 | MATLAB | 1,018 | 25 | function [c,ld] = lagrangian_foopsi_temporal(y,a,thr,G,ld_in)
% solves min sum(G*c)
% s.t.: G*c >= 0, ||a(j)*c - y(j)|| <= thr(j)
T = size(G,1);
la = length(a);
myfun = @(Ald) lagrangian_temporal_grad(Ald,y,thr);
options = optimset('GradObj','On','Display','Off','Algorithm','interior-point','TolX',1e-6);
if nar... |
927f5ba1a68b4b56c80bcab2a35a6d191eb70576577e6ad8995baf62887232ee | MATLAB | 1,019 | 28 | function mappedX = mds(X, no_dims)
%MDS Run MDS on the data to get a low-dimensional visualization
%
% mappedX = mds(X, no_dims)
%
% Run multidimensional scaling on the dataset X to get a two-dimensional
% visualization. The low-dimensional representation is returned in mappedX.
% It has dimensionality no_dims (def... |
1e97b05fa68ccb5eea73bb963fb4d39187f5b963fb818edfbea55c4c8d95c389 | MATLAB | 1,025 | 30 | function rho=dispersionCoefficient(C)
% Calculate the dispersion Coefficient
% This function is called by function "chooseBestk"
% C: matrix, the relation matrix
% rho, scalar, the score
%%%%
% Copyright (C) <2012> <Yifeng Li>
%
% This program is free software: you can redistribute it and/or modify
% it under the ter... |
d2eed0693660ff1135f206dca9e9feb2a852b9e4430103506ffa14492e9b52de | MATLAB | 1,026 | 25 | function param = KAPPA(TP, TN, FP, FN, param)
% =========================================================================
% function param = KAPPA(TP, TN, FP, FN)
% =========================================================================
% Compute Cohen's Kappa based on contigency matrix
% %%%%%%%%%%%%%%%%%%%%%%%%%%%... |
d809fde32ab6a3a7e21a5f313c9b2a10973bcd52b5e8bf3bdd1d2282783b8948 | MATLAB | 1,029 | 39 | function set_meanFR
% SET_MEANFR Mean firing rate
% SET_MEANFR stores mean firing rate property of all detected units in CellBase
% Balázs Hangya, Johanna Petra Szabó, 10.2024
% Lendulet Laboratory of Systems Neuroscience
% Institute of Experimental Medicine, Budapest, Hungary
% szabo.johanna@koki.hun-ren.h... |
33627b725ef4e0628e85de8ee93ba9ff266ec2f5f65b42b488c0d1feac8bd03d | MATLAB | 1,034 | 45 | function h = condentropy(vec1,vec2)
%=========================================================
%
%This is a prog in the MutualInfo 0.9 package written by
% Hanchuan Peng.
%
%Disclaimer: The author of program is Hanchuan Peng
% at <penghanchuan@yahoo.com> and <phc@cbmv.jhu.edu>.
%
%The CopyRight is reserved by the... |
1c3515ac571bfbf010808397b86f9ae93b0cff1476faa77df54b9880c5595fa1 | MATLAB | 1,035 | 38 | function [ROIMEANS, act ] = cv_ROImeans_config(ROIMEANS, brainmask, parentstr, defaultsfl)
Atlas = [];
if ~exist('defaultsfl','var') || isempty(defaultsfl); defaultsfl = false; end
if ~defaultsfl
if isfield(ROIMEANS,'atlas') && ~isempty(ROIMEANS.atlas)
Atlas = ROIMEANS.atlas;
end
if ~isempty(Atl... |
8a66e19911cc68a057aa70bc2cc0d0d9063fb01b144d6c012362401420de9b12 | MATLAB | 1,036 | 40 | function H = nk_Entropy(P, vec, m, n)
% ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
% function H = nk_Entropy(P, vec, m, n)
% ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
%
% Compute entropy-based measure of ensemble diversity
%
% Inputs:
% =======
% P = Input matrix
% vec = unique values in input matrix
% m = # of rows i... |
9e58671a7bd6210c548a179fa4721d6ceed24d89d1f0f3d288541870872520c5 | MATLAB | 1,037 | 37 | function op = prox_l1( q )
%PROX_L1 L1 norm.
% OP = PROX_L1( q ) implements the nonsmooth function
% OP(X) = norm(q.*X,1).
% Q is optional; if omitted, Q=1 is assumed. But if Q is supplied,
% then it must be a positive real scalar (or must be same size as X).
% Dual: proj_linf.m
% Update Feb 2011, ... |
2f3d414ae0d1f7fc2a9ed90741b3a089593f1f8de694ec9c703ee4b771b3da80 | MATLAB | 1,038 | 39 | function CutterOption_AllCrossCorrs(self)
% shows crosscorrs of shows
%
% INPUTS
%
% OUTPUTS
%
% NONE
% ADR 2013
%
% Status: PROMOTED (Release version)
% See documentation for copyright (owned by original authors) and warranties (none!).
% This code released as part of MClust 3.0.
% Version control M3.0.
% Extensiv... |
87f8c8601767b5cbb5790e5766256fd2eb1fb1748667404892e4a3219f57ef9c | MATLAB | 1,039 | 28 | % Bins probability estimates and also returns the empirical probability
% estimate within each bin
function [pDisc, empProb] = binProbabilities(p, y, gridSize)
% Sort probability estimates in increasing order
p = reshape(p, [1 numel(p)]);
[p, i] = sort(p, 'ascend');
y = y(i);
pDisc = round... |
360024411a6dfcbef69a79f58596bba0a49df1552abe809c175e6ca440c3bf2c | MATLAB | 1,040 | 30 | currdir = fullfile(pwd)
cmd.savePath = currdir
[PATHSTR,NAME,EXT] = fileparts(cmd.files.viewpoint{1})
cmd.files.viewpoint{1} = fullfile(pwd,[NAME EXT])
[PATHSTR,NAME,EXT] = fileparts(cmd.files.grouping{1})
cmd.files.grouping{1} = fullfile(pwd,[NAME EXT])
[PATHSTR,NAME,EXT] = fileparts(cmd.files.timing{1})
cmd.files.... |
1aaefcf137f5bf6a1f1e0e2d07c35bd564480e5b73cb39b0e05bf5b063088f42 | MATLAB | 1,043 | 33 | function sc = datpointsplot(dat,gooddat,lab,color)
% DATPOINTSPLOT Dots overlayed on boxplots
% DATPOINTSPLOT(dat,gooddat,lab,color) adds randomly scattered dots
% corrsponding to each datapoint. Should be plotted over boxplots.
%
% Input parameters:
% DAT MxN matrix, M: nr of datapoints, ... |
eea5bba504815f9c06111ff4f48fa794376fe7ab7d97a6f5ca07573ec62bc335 | MATLAB | 1,043 | 37 | function [tfFull,tf,n]=iszero(a)
% if vector a is zero vector then tf=true, if a(i)==0, then tfFull(i)=true,
% else =false.
% n: number of zero elements
%%%%
% Copyright (C) <2012> <Yifeng Li>
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public Licen... |
8f575d6457ccacf2aa1ca145528c5501fd009764564c7148ee7996130667b7bc | MATLAB | 1,044 | 46 | function [varargout] = mbm_plot_map(axisPlot, vertices, faces, dataToPlot, hemis, isCbar)
% plot measurement on a surface
%
%% Inputs:
% axisPlot - axis to plot on
%
% vertices - vector of vertices
%
% faces - matrix of faces (3 columns)
%
% dataToPlot - vector of data to plot
%
% hemis - '... |
be0803ca3633d6703ff683398f8ab1b3a5cb55e542c3631c5b01d89b375a710a | MATLAB | 1,044 | 40 | % NDMwS
%
% Evaluate NDMwS predictions [y] at desired time stamps.
%
% Input:
% x0 = Initial Condition
% time_stamps = provided in units given by experiment
% C = connectivity matrix
% beta = diffusivity parameter
% alpha0 = cte growth/decay term independe... |
41e35be5b1265defd8b5cafb485ffe16e4132eab0c2296ea2aa42a41cc9e3af0 | MATLAB | 1,045 | 49 | function [AC,xr] = AutoCorr(T, varargin)
% MClust.AutoCorr(T)
%
%
% INPUTS
% T -- times of data (in seconds)
%
% OUTPUTS
% AC --- tsd of autocorrelation of self
%
% ADR 2012
%
% Status: PROMOTED (Release version)
% See documentation for copyright (owned by original authors) and warranties (none!).
% This code re... |
102128330bb823d58af7d2641d904c6d8e24e4d00210851d687fd764f53bd64c | MATLAB | 1,046 | 30 | % CL Septembre 2022, landelle.caroline@gmail.com // caroline.landelle@mcgill.ca
% Toolbox required: Matlab, SPM12
%%
function Norm=Norm_BMPD(filename_DeformField,filename_func,SPM_Dir)
%______________________________________________________________________
%% Initialization
%______________________________________... |
a4d8279806c96b61563d38e4e9658033640f478e4b85d7bec46b06ddb886e376 | MATLAB | 1,047 | 43 | function hdr = encode_qform0(M,hdr)
% Encode an affine transform into qform
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
% $Id: encode_qform0.m 7147 2017-08-03 14:07:01Z spm $
% Convert from first voxel at [1,1,1] to fi... |
112e3787bb9b2f64a32018dfd996809ad602d89799dea8f61dbfa303665b92e2 | MATLAB | 1,049 | 39 | function [n,names] = plx_event_names(filename)
% plx_event_names(filename): gets the names of event channels in a .plx file
%
% [n, names] = plx_event_names(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% names - array of event name strings
% n - number of channels
if n... |
d6b867dd309ca5c84df2b1769f5cd2e30c53a639bb6afa3859efa3792245b0a7 | MATLAB | 1,049 | 44 | function WriteHeader(fp, varargin)
% WriteHeader(fp, H1, H2, H3, ...)
%
% INPUTS
% fp = file pointer
% H1, H2, H3, ... = lines (strings) to write out as header
%
% OUTPUTS: none
%
% Writes NSMA header
%
% ADR 1998
% version U3.1
% status PROMOTED
MCS = MClust.GetSettings();
% v 3.1 now accepts cell arrays a... |
9aaf8480c5356b3cc4d33ef4c73ac53651c562c36e68a68b24d982466fa434c2 | MATLAB | 1,050 | 40 | function varargout = fname(varargin)
% file_array's fname property
% For getting the value
% dat = fname(obj)
%
% For setting the value
% obj = fname(obj,dat)
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
% $Id: fname.m 71... |
b01690e5b412a99a573a663622c7f7ba8a280734b7f19308fa9c7d2126f4a9b7 | MATLAB | 1,050 | 28 | function scores = corrcoef_select(X_train, Y_train);
% scores = corrcoef_select(X_train, Y_train);
%
% Implementation of correletion coeficient feature selection, as used in:
%
% A. Navot, L. Shpigelman, N. Tishby, E. Vaadia. Nearest Neighbor Based Feature Selection for Regression and its
% Application to Neural Act... |
b107c9c0facb97f6ac7a157dac7c80a29000854aa8837268b59f4f73a123003f | MATLAB | 1,051 | 45 | function [T, Thresh] = nk_Threshold(V, thresh)
if thresh.type ~= 3
sig = false(size(V,2),1);
switch thresh.type
case 1
% Percentile method
Thresh = percentile(V, thresh.val);
case 2
% Absolute threshold
Thresh = thresh.val;
end
... |
0cc31ebf625308eab8c4422539adb2f87aa147f9d9273ca545d9e15596fc1eb7 | MATLAB | 1,052 | 23 | function [L, targscale, Lmin, Lmax, Lfact, Lpolyfact, Llogar] = nk_LabelTransform(Param, MODEFL, L)
targscale = 0; Lmin = min(L); Lmax = max(L); Lfact = 1; Lpolyfact = []; Llogar = [];
if isfield(Param,'LABELMOD') && strcmp(MODEFL,'regression')
if isfield(Param.LABELMOD,'TARGETSCALE') && Param.LABELMOD.TARGETSCAL... |
8cef6fc4d705dcc2edd5aeab707db18be98fb11f42431dcd364e22cb61ddb656 | MATLAB | 1,052 | 40 | % NDMwS
%
% Evaluate NDMwS predictions [y] at desired time stamps.
%
% Input:
% x0 = Initial Condition
% time_stamps = provided in units given by experiment
% C = connectivity matrix
% beta = diffusivity parameter
% alpha1 = linear growth/clearance term in... |
9ee504651dceb65d4fffbb02df4e91749793477769a9378c19e2177831fc7a04 | MATLAB | 1,055 | 23 | function mess = CheckImageInfoConsistency(Vinfo, Vvox, mess)
if ~exist('mess','var'), mess=[]; end
% Check translational
H = size(unique(Vinfo(:,1:3),'rows'),1);
if H>1, mess = GenerateMessageEntry(mess, 'WARNING: Images do not have the same translation parameters.', 2, 'SystemCommands'); end
% Check rotation
R = s... |
8dd6707f90077402b8369ca2d1e34f01e1ecff37c712059c9761fff54115f6d0 | MATLAB | 1,057 | 42 | function [res] = lmc(x)
%LMC calculates the left medcouple, a robust measure of
%left tail weight
%
% The left medcouple is described in:
% Brys, G., Hubert, M. and Struyf, A. (2006),
% "Robust Measures of Tail Weight",
% Computational Statistics and Data Analysis,
% 50 (No 3), 733-759.
%
% For the up-to-... |
117d8db47f22de8fbec28a8bac11f056947d8499a50c825cfc78f0030c14f00c | MATLAB | 1,058 | 41 | function chiqqplot(y,p,class)
%CHIQQPLOT produces a Quantile-Quantile-plot of the vector y
% versus the square root of the quantiles of the chi-squared distribution.
%
% Required input arguments:
% y : row or column vector
% p : degrees of freedom of the chi-squared distribution
%
% Optional input arg... |
377d10e4b8ccc8783077074ff5632018461637e345b70eff69ff6d9289e0ca3e | MATLAB | 1,059 | 27 | function s = spm_existfile(filename)
% Check if a file exists on disk - a compiled routine
% FORMAT s = spm_existfile(filename)
% filename - filename (can also be a relative or full pathname to a file)
% s - logical scalar, true if the file exists and false otherwise
%____________________________________________... |
7856da1e0ab4b62d59be22f1a52fb351453c683c4712ba66847024d12cc8e331 | MATLAB | 1,061 | 43 | function [res] = rmc(x)
%RMC calculates the right medcouple, a robust measure of
%right tail weight
%
% The right medcouple is described in:
% Brys, G., Hubert, M. and Struyf, A. (2006),
% "Robust Measures of Tail Weight",
% Computational Statistics and Data Analysis,
% 50 (No 3), 733-759.
%
% For the up-... |
772a23ad84a0016c396c3c302a056e0d798014939d9434c121aa4e5be4642183 | MATLAB | 1,065 | 38 | function [channelNumber] = plx_resolve_channel(filename, channel)
% plx_resolve_channel(filename, channel): returns .plx file spike channel number for the specified channel name
%
% [channelNumber] = plx_resolve_channel(filename, channel)
%
% INPUT:
% filename - file name
% channel - 1-based channel number or chann... |
c9ad9f079f4205594bdb48d106eef7577f95ab2ce49a7ebc6d296f34bf8b6b35 | MATLAB | 1,065 | 33 | function model=logisticRegressTrain(trainSet,trainClass,option)
% logistic regression for classification
%%%%
% Copyright (C) <2012> <Yifeng Li>
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundati... |
e8c29a5499285a18b0dbd53c71bc8e029b0687b45165c937f5f9c5490db48907 | MATLAB | 1,070 | 34 | function [ts] = PL2TsBySource( filename, source, channelInSource, unit )
% PL2TsBySource( filename, source, channelInSource, unit ): read spike timestamps from a .pl2 file
%
% ts = PL2TsBySource( filename, source, channelInSource, unit );
% ts = PL2TsBySource( filename, 'SPK', 1, 2 );
% ts = PL2TsBySource( filename, 7,... |
fa26dc6fedbc3fe8c08270dbfb51af603b669a87de20009f067cf9d05314ceda | MATLAB | 1,072 | 33 | function [Y,numIter,tElapsed]=seminmfnnlstest(X,outTrain)
% Project test samples into the feature space, this function is called by
% function featureExtractionTest.
%%%%
% Copyright (C) <2012> <Yifeng Li>
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General... |
6552b11a15b9d3dd4d63b52084bbb26662aae55380efc61ed25b660162eb34f5 | MATLAB | 1,074 | 26 | % Given new scores yHat, and a mapping yHatIR -> yIR, calibrates the scores
% in yHat
function yCal = calibrateScores(yHat, yHatIR, yIR)
n = length(yHatIR);
[v,i] = sort(yHatIR);
yHatIR = yHatIR(i); yIR = yIR(i);
yCalIdx = bsearch(yHatIR, yHat);
delta = yHat - yHatIR(yCalIdx); %disp('delta:'... |
a8efc56eea6a88cd2fd35ba4272bb37a79aa606c85d714bbd2e49a13f76b0ef2 | MATLAB | 1,075 | 33 | function [Lrand,Crand] = NullModel_L_C(n,m,Nrepeats,FLAG)
% NULLMODEL_L_C Monte Carlo estimates of path-length and clustering of an ER random graph
% [C,L] = NULLMODEL_L_C(N,M,R,FLAG) for N nodes and M edges,
% creates R realisations of an Erdos-Renyi random graph (N,M), and
% computes the shortest path-length L and c... |
f2f1c8b34c2f21bb78d838f07c3d6dcadf081988be70f8e5054a0bbbf561ab4e | MATLAB | 1,079 | 39 | function []=run_spm_glm_stage_1(subject)
addpath('~/apps/spm12');
spm('Defaults', 'fMRI');
setenv('SPM_HTML_BROWSER','0');
spm_jobman('initcfg');
spm_get_defaults('cmdline',true);
home = getenv('HOME');
data_dir = [home,'/data/multimodal_decoding/fmri/bids/derivatives/betas/', subject, '/un... |
a12c621ea9f8379c7f3bff3c685b71274286a99b29f8ee8dce8c424edf5506b1 | MATLAB | 1,080 | 25 | function welcome
%WELCOME Displays DR Toolbox version information
%
% welcome
%
% Displays DR Toolbox version information.
% This file is part of the Matlab Toolbox for Dimensionality Reduction.
% The toolbox can be obtained from http://homepage.tudelft.nl/19j49
% You are free to use, change, or redistribute this co... |
ea76fb3528297510a0804c255f4de8519ca860f33e3290ef06b3101685cf015a | MATLAB | 1,080 | 37 | function [C, cAUC] = nk_CreatPredFeat(AUC_upper, AUC_lower, L, verbose)
cAUC = 0;
c1_x0_rng = linspace(0, .25, 5); c1n = numel(c1_x0_rng);
c2_x0_rng = linspace(-0.25, 0, 5); c2n = numel(c2_x0_rng);
w_st = 0.5; w_end = 1.5;
c_w_rng = linspace(w_st, w_end, 5); cwn = numel(c_w_rng);
c1_caseN = sum(L==1);
c2_caseN = sum(L... |
2d9613f08631e0458e124ff0f29f208f14d46c207c64348ec69c5ff7e8002b71 | MATLAB | 1,081 | 34 | function [coreness,kn] = kcoreness_centrality_bu(CIJ)
%KCORENESS_CENTRALITY_BU K-coreness centrality
%
% [coreness,kn] = kcoreness_centrality_bu(CIJ)
%
% The k-core is the largest subgraph comprising nodes of degree at least
% k. The coreness of a node is k if the node belongs to the k-core but
% not to ... |
fec1dbff845f4612cfd3c7d6b7916609de874c2472f09651775da1352e385205 | MATLAB | 1,082 | 29 | function frame = msReadFrame(ms,frameNum,columnCorrect, align, dFF)
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
vidNum = ms.vidNum(frameNum);
vidFrameNum = ms.frameNum(frameNum);
if ms.vidNum(1)==0
frame = double(ms.vidObj{vidNum+1}.read(vidFrameNum));
... |
8a89acb7375e677549253f1353a7530f7fffcafe8e6372ad66f3f158301f384a | MATLAB | 1,083 | 34 | function Pk=EQP(H,C,X,W,lambda)
% solve the equality constrained QP
% Yifeng Li, Feb. 21, 2012
option.tol=0;%2^(-32);
[nV,nP]=size(X);
% code=2.^(2*nV-1:-1:0) * W;
code=genCode(W);
% [codeSorted,csInd]=sort(code);
codeUnik=unique(code);
numUnik=numel(codeUnik);
Pk=zeros(2*nV,nP);
for i=1:numUnik
indLog=(code==codeU... |
e3cdb4b4271545065d5d6c8fdbf5ed47c094fe8ced023b2484a5eb4544be5a5e | MATLAB | 1,083 | 39 | function [ranset,seed]=randomset(tot,nel,seed)
%RANDOMSET draws randomly a subsample of nel cases out of tot.
%(It is called if not all (p+1)-subsets out of n will be considered.)
%
% Required input arguments:
% tot : The total number of observations to consider
% nel : The number of observations that the su... |
a81cff7a4eaeb6b3ec9ea4863028e127d9bb4a648ee470e3df9306db55bafb5b | MATLAB | 1,084 | 37 | % =========================================================================
% FORMAT [mED, ED] = nk_Lobag(E, L)
% =========================================================================
% This function performs the bias / variance decomposition of the error
% proposed by Valentini & Dietterich (2004, Journal of Mach... |
526c5a5f2a5888d6aeb8949245e02552c725a7533384a6f86672ff55e852185e | MATLAB | 1,085 | 31 | function M = nk_ConcatSubgroupPredictions
% This script assumes that you have run each subgroup model on the training & CV data (the
% subgroup) and the independent test data (the rest of the population
% stored in NM.OOCV{1}). The analysis should be in NM.analysis{1}
% The following statements should concatenate the ... |
64776811c0d5384d90fbc83e3bc10ba278e654f9d59608f19dc2a67085060eef | MATLAB | 1,088 | 39 | function varargout = scl_inter(varargin)
% file_array's scl_inter property
% For getting the value
% dat = scl_inter(obj)
%
% For setting the value
% obj = scl_inter(obj,dat)
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
%... |
53c8fd2ed31392d704a7aa5a458c7c7eba33da2be9d6b5bb4f8846a0427e9842 | MATLAB | 1,090 | 40 | function varargout = scl_slope(varargin)
% file_array's scl_slope property
% For getting the value
% dat = scl_slope(obj)
%
% For setting the value
% obj = scl_slope(obj,dat)
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
%... |
15feb3b63c9973934469270381132074a7289fa5d0720410258bcc51519b423c | MATLAB | 1,091 | 33 | %% FUNCTION LSSMTC
% Transform the partition matrix to clustering results
%
%% LICENSE
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your op... |
1f6d75ba695c3c85de30fb25cabf432c3fd498c48298ea4c9d3428af0bd67e52 | MATLAB | 1,092 | 28 | function reconX = recon_data_from_autoenc(network, mappedX)
%RUN_DATA_THROUGH_AUTOENC Summary of this function goes here
% Detailed explanation goes here
% This file is part of the Matlab Toolbox for Dimensionality Reduction.
% The toolbox can be obtained from http://homepage.tudelft.nl/19j49
% You are free to use, ... |
cd421f9cc73c570eb8976e428dd0cc331531056c220d9ce3eb6e589362103fc9 | MATLAB | 1,094 | 28 | function reconX = recon_data_from_autoenc2(network, mappedX)
%RUN_DATA_THROUGH_AUTOENC Summary of this function goes here
% Detailed explanation goes here
% This file is part of the Matlab Toolbox for Dimensionality Reduction.
% The toolbox can be obtained from http://homepage.tudelft.nl/19j49
% You are free to use,... |
ed87dec9e24259042b0b872866532f91843952be1d644abde2074435c9986687 | MATLAB | 1,096 | 41 | function Z=module_degree_zscore(W,Ci,flag)
%MODULE_DEGREE_ZSCORE Within-module degree z-score
%
% Z=module_degree_zscore(W,Ci,flag);
%
% The within-module degree z-score is a within-module version of degree
% centrality.
%
% Inputs: W, binary/weighted, directed/undirected connection matrix
% ... |
396b68160bd546744a6c8a9f25e0253becaf33cb97ecb72f46974f43fc3bd25b | MATLAB | 1,097 | 33 | function [GEdiff,Ediff] = diffusion_efficiency(adj)
% DIFFUSION_EFFICIENCY Global mean and pair-wise diffusion efficiency
%
% [GEdiff,Ediff] = diffusion_efficiency(adj);
%
% The diffusion efficiency between nodes i and j is the inverse of the
% mean first passage time from i to j, that is the expected number... |
3afc6760e7071801f75562dfabc6e09ff0026d60e985de46c65f83e2176ca209 | MATLAB | 1,098 | 33 | function [event] = PL2EventTsBySource(filename, source, channelInSource)
% PL2EventTsBySource(filename, source, channelInSource): read event timestamps from a .pl2 file
%
% [event] = PL2EventTs(filename, source, channelInSource)
% [event] = PL2EventTs(filename, "KBD', 1)
% [event] = PL2EventTs(fi... |
53a419c099e0f54c84a341f79bedb13c78bf0e45b4230c67ab6b3a282fa84d95 | MATLAB | 1,099 | 45 | function newvariable = mergemultivariables(variablearray1,variablearray2)
%=========================================================
%
%This is a prog in the MutualInfo 0.9 package written by
% Hanchuan Peng.
%
%Disclaimer: The author of program is Hanchuan Peng
% at <penghanchuan@yahoo.com> and <phc@cbmv.jhu.edu... |
6cd752d91581da7987fe79a428495eba1d7d858240e196f65b457eab7fc85c97 | MATLAB | 1,099 | 34 | function set_visibility(handles)
if ~handles.NM.analysis{handles.curranal}.status || (sum(handles.MLparams.NumParamCombs) <= handles.nclass && ~isfield(handles,'visdata'))
vis = 'off';
else
vis = 'on';
end
set(handles.pnModelPerf,'Visible',vis);
set(handles.selModelMeasures,'Enable',vis);
switch handles.mode... |
0911b66d9ab1ceca35f7fc739686705be4fb410199d9a427b51e9df4710758d5 | MATLAB | 1,100 | 46 | function RegulFunc = nk_RegulFunc_config(defaultfl)
if ~exist('defaultfl','var') || isempty(defaultfl)
defaultfl = false;
end
if ~defaultfl
RegulType = nk_input('Regularization function',0,'m', ...
['none|', ...
'1 - values|', ...
'cosinus|', ...
'sinus|', ...
'1 -... |
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