sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3a5114e042f0ba248fe6b496e95bac7b39d992fdf718815cff8d078b9e1ef7b7 | MATLAB | 1,670 | 41 | function y = fwdpr1(Lden, b) %#ok
% y = fwdpr1(Lden, b)
%
% FWDPR1 Solves "PROD_k L(pk,betak) * y = b", where
% where L(p,beta) = eye(n) + tril(p*beta',-1).
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi, dpr1fact, bwdpr1
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Rom... |
7db0957c0e953f7c2a3147f14277463c37d3660642cd3144ad045aa860649a86 | MATLAB | 1,670 | 70 | function result = cvelnet(object, lambda, x, y, weights, offset, foldid, ...
type, grouped, keep)
% Internal glmnet function. See also cvglmnet.
if nargin < 10 || isempty(keep)
keep = false;
end
typenames = struct('deviance','Mean-Squared Error','mse','Mean-Squared Error','mae','Mean Absolute Error');
if str... |
ae8a86577b45c2e8ee983551ff97423b6533fe75098878f36ec62231da41ab1d | MATLAB | 1,670 | 40 | function Ablkjc = partitA(At,blkstart) %#ok
% Ablkjc = partitA(At,blkstart)
%
% PARTITA Partition columns of A according to the subscripts listed in blkstart.
%
% ******************** INTERNAL FUNCTION OF SEDUMI ********************
%
% See also sedumi
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr Rom... |
f5d588005cf72b271238a1efff7fa768b9b9fadf2a060396034939aa377e40e2 | MATLAB | 1,671 | 75 | function fit = elnet(x, is_sparse, irs, pcs, y, weights, offset, gtype, ...
parm, lempty, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, ...
isd, intr, maxit, family)
ybar = y' * weights/ sum(weights);
nulldev = (y' - ybar).^2 * weights;
ka = find(strncmp(gtype,{'covariance','naive'},length(gtype)),1);
... |
6167d10a488ec38dacc3820dc865ed3904ac53bb48ed87d6b40a4c7df2c6078c | MATLAB | 1,672 | 48 | function minimametric = metric_minima_all_cifti(metric,neighdist,neighbors)
if ~exist('neighbors')
bufsize=16384;
% Read in node neighbor file generated from caret -surface-topology-neighbors
[neighbors(:,1) neighbors(:,2) neighbors(:,3) neighbors(:,4)...
neighbors(:,5) neighbors(:,6) neighbors... |
b43df54730feff3fedfe339c50ee3dea82c5c5373facc52f9d84ff88d70b7fc8 | MATLAB | 1,672 | 79 | function y = square( x )
%SQUARE Internal cvx version.
% 0 : all others
% 1 : constant
% 2 : real affine
% 3 : monomial, posynomial
narginchk(1,1);
persistent remap
if isempty( remap ),
remap1 = cvx_remap( 'constant' );
remap2 = cvx_remap( 'affine' ) & ~remap1;
remap3 = cvx_remap( 'log-valid' ) & ~remap... |
80df12133ae5f72c233b010efbbcfd732e7ba0d197f12b88bf2fb693156358b4 | MATLAB | 1,673 | 64 | classdef ProgressTracker < handle
properties
count = 0
total = 0
lastPrint
startTime
end
methods
function obj = ProgressTracker(total)
obj.total = total;
obj.lastPrint = tic;
obj.startTime = tic;
end
function update(o... |
8bd9f68dbe6784a3ac08f8ce375355e9db1d4cfc4df718f05d187d2df0737ba6 | MATLAB | 1,673 | 78 | function [code, name, rgbv] = read_fscolorlut(fname)
% [code name rgb] = read_fscolorlut(fname)
%
% Reads a freesurfer color lookup table. By default
% reads $FREESURFER_HOME/FreeSurferColorLUT.txt.
%
%
% read_fscolorlut.m
%
% Original Author: Doug Greve
% CVS Revision Info:
% $Author: fischl $
% $Date: 2008/04... |
8dfe71503597e13c5385dfbb764802a24f45747e4fa929b5f56b9d0114dcdcff | MATLAB | 1,673 | 39 | function plotSubpopCompContoursCCF(dorsalMaps, allROIs, model, smoothSD, contConfig)
% Plots contours for the likelihood values obtained from area-specific
% components that have been clustered into a subpopulation
% Figure
allenMapSMc(dorsalMaps, [-3.6, 0, -2, 3]) % Creates figure by itself
% Plot params
xLimits = [... |
d56d649f143427448042e2da277472aac194e13d6305da010df06d4f5adf630d | MATLAB | 1,673 | 50 | function ea_cat_seg(options)
options.prefs=ea_prefs;
[options,presentfiles]=ea_assignpretra(options);
job.data = {[options.root,options.patientname,filesep,presentfiles{1}]};
job.nproc = 0;
job.opts.tpm = {[ea_space,'TPM.nii']};
job.opts.affreg = 'mni';
job.opts.biasstr = 0.5;
job.extopts.APP = 1070;
job.extopts.LAS... |
9d620285cf21e44d9cc8f2ff38b734e406695ce5f94f62bb9f6291ba2dd26db8 | MATLAB | 1,674 | 52 | function [betas, stats] = CBIG_fitGLM_2t(subInfoFile, GMICVFile, q)
% [betas, stats] = CBIG_fitGLM_2t(subInfoFile, GMICVFile, q)
% What is the subtype order?
% Offset by 1, the RID column
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
COR_COL = 1+1;
fprintf('\n\n\n'... |
a35fd250d4ded6f1918b669afa5da3cd0593e1c8fd6a15b79f3c0e55c1a1fcbc | MATLAB | 1,674 | 56 | function [stimname,preexist]=ea_detstimname(options)
preexist = 0;
% check if previous stimulations have been stored
if ~isfield(options,'root') % called from lead group
stimname = ['gs_',options.groupid];
return
end
stimname = cell(0);
if exist([options.subj.stimDir, filesep, ea_nt(options)],'dir')
stimd... |
c6806f6bc099a49acd0ae3a2c3b60c7267e63d2371248926c3d98629f27ba962 | MATLAB | 1,674 | 64 | function r = circ_r(alpha, w, d, dim)
% r = circ_r(alpha, w, d)
% Computes mean resultant vector length for circular data.
%
% Input:
% alpha sample of angles in radians
% [w number of incidences in case of binned angle data]
% [d spacing of bin centers for binned data, if supplied
% corr... |
c68146d196af3ab2a37ba7d824cbdd5fb3a24b2567f9dc6bd40dc2f69a957719 | MATLAB | 1,674 | 56 | %issamples - Test if parameter is a list of samples satisfying an optional list of tests.
%
% A list of samples is a vector or matrix of doubles containing at least one column
% for timestamps, and optionally more for continuous variables.
%
% USAGE
%
% test = issamples(x,test1,test2,...)
%
% x pa... |
351460514fdc77ff4cf90ddc330abcaa59ab311d9962bb994ef62c865b54d79b | MATLAB | 1,675 | 53 | % Go to main project directory before running. Uses current dir as main
% project dir.
% Set paths and directories
canlab_simple_set_paths;
%% Load DAT structure with setup info
% ------------------------------------------------------------------------
savefilename = fullfile(resultsdir, 'image_names_and_setup.mat')... |
dfdf4e84ae48765030b4cf3168619bb6f76bf5bcf48b010d8b760085b00793d5 | MATLAB | 1,675 | 69 | %RunBatch - Run a batch job. This should *not* be called directly.
%
% Run a batch job. This function is called automatically by the
% batch timer upon expiration of the required delay.
%
% USAGE
%
% RunBatch(timer,event,b)
%
% timer Matlab timer object
% event Matlab timer event type
% b... |
2cd5ada6dd5914d3f266cdfd74752b3b8497aaad87b98e02d502b2047966985d | MATLAB | 1,676 | 63 | function v = cvx_class( x, needsign, needreal, needzero )
if nargin < 2, needsign = false; end
if nargin < 3, needreal = false; end
if nargin < 4, needzero = needsign; end
% Classifications:
% 1 - negative constant
% 2 - zero
% 3 - positive constant
% 4 - complex constant
% 5 - concave
% 6 - real affi... |
3248496b93abf26fe686dbd530c8b65efa33753ec6360501ba41133dbb3d1d9f | MATLAB | 1,676 | 42 | function [zhi,zlo] = quadadd(xhi,xlo,y) %#ok
% [zhi,zlo] = quadadd(xhi,xlo,y)
%
% QUADADD Compute (zhi+zlo) = (xhi+xlo) + y.
% x an z are in double-double format (quad precision)
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by Imre Polik and Oleksandr... |
65ea11af45ed310b97820a667aecd29fab54da68632428e92d76bf46d3bb00bd | MATLAB | 1,676 | 35 | mainfolder0 = '/Users/yiyuan/OneDrive - University of Essex/PG Research/0A_Journal/202004_unknown Journal_Probability Score/1_Results/0_Final Results/Results_Main/';
figurefolder = '/Users/yiyuan/OneDrive - University of Essex/PG Research/0A_Journal/202004_unknown Journal_Probability Score/1_Results/0_Final Results/Res... |
d87889c7ff290f99a91e704a94ae69a1d568650be04f1ba4c47d7a6d21986de7 | MATLAB | 1,676 | 45 | % Verify NIFTI header extension to make sure that each extension section
% must be an integer multiple of 16 byte long that includes the first 8
% bytes of esize and ecode. If the length of extension section is not the
% above mentioned case, edata should be padded with all 0.
%
% Usage: [ext, esize_total] = verif... |
ff4a1fce844522b5d9c5ee4af8501369ee478fa9e9f72947cad71b07218363c9 | MATLAB | 1,676 | 47 | function [pca_regs_Hb, pca_regs_OD, diag_info] = pick_pca_regs(HBO, HBD, dOD_hp, conv, n_pca, r2max)
%NIRSPROC.PICK_PCA_REGS Select task-uncorrelated PCs as nuisance regressors.
% [pca_regs_Hb, pca_regs_OD, diag_info] = NIRSPROC.PICK_PCA_REGS(...)
%
% Inputs
% HBO, HBD : T×nCh HbO/HbR time series
% dOD_h... |
37cda8e4e0b335bb9018984a6c98aa0f54de34c27c54f13da03d9764b5613cc6 | MATLAB | 1,677 | 49 | function done = ea_coregpostopct(options)
% Entry function to coregister post-op CT to pre-op MRI
done = 0;
if ~ea_reglocked(options, options.subj.postopAnat.CT.coreg)
% Setup log
if options.prefs.diary
ea_mkdir(fileparts(options.subj.coreg.log.logBaseName));
diary([options.subj.coreg.log.logB... |
bb7c7e34c7aa81f1906688b81149674bdba987d35ca266531a859af33a14d267 | MATLAB | 1,677 | 53 | %%************************************************************
%% Prod3: compute the entries of Q = A*B*C specified in
%% nzlistQ.
%%
%% Q = Prod3(blk,A,B,C,sym,nzlistQ)
%% Important: (a) A is assumed to be symmetric if nzlistQ
%% has 2 columns (since mexProd2nz computes A'*B).
%% (b) T... |
b03e54a167661b2810782b34e55a4f6111da4d62c7dcbce82917780fe5bda863 | MATLAB | 1,678 | 48 | function [out, G] = filterGauss2D(image, sigma, borderCondition)
% filterGauss2D : filters an image with a 2-D Gaussian mask
%
% [out, G] = filterGauss2D(image, sigma, borderCondition);
%
% INPUT: image : 2-D input array
% sigma : standard deviation of the Gaussian
% ... |
bb9afd80a4bd9dd271d99c0b2195de891e5dc50025a8303fba8951c3f2334ba5 | MATLAB | 1,678 | 51 | function ea_show_light(resultfig,viz)
% if viz = 1; turn on
% if viz = 0; turn off
% default viz=1;
if nargin<2
viz=1;
end
set(0,'CurrentFigure',resultfig);
prefs = ea_prefs;
CamLight=light('style','infinite','Color',prefs.d3.camlightcolor); % not modifiable, infinite light.
%set(cam_lamp,'Color',[1,1,1]);
camli... |
d8652eb72419ec8bdbc089abae73fb76ca93a75ab4cc1007a02eb9a0cdd8e632 | MATLAB | 1,678 | 34 | % SOFA API - demo script
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences
% Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "License")
% You may not use this work except in compliance with t... |
574a4be0bf641c17128dc1808f72aa29e8c78b91619c2048c5f40221cc464918 | MATLAB | 1,680 | 53 | function [betas, stats] = CBIG_fitGLM_3t(subInfoFile, GMICVFile, q)
% [betas, stats] = CBIG_fitGLM_3t(subInfoFile, GMICVFile, q)
% What is the subtype order?
% Offset by 1, the RID column
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
SUB_COL = 1+3;
COR_COL = 1+1;
f... |
adf6f392a9f956f8e6d66e8cba0c0d3103b7cb6351e7e76a2240e6f7820dd1d8 | MATLAB | 1,680 | 46 | function writeMoCorTifs(files,moCorImgData,outputPath)
%prevents printing of irrelevant tif header errors
warning('off','MATLAB:imagesci:tiffmexutils:libtiffWarning');
fStart = 1;
for fileNo = 1:length(files)
tmpImInfo = imfinfo([files(fileNo).folder filesep files(fileNo).name]);
nFrames = length(tmpImI... |
09ef6230f1c61faf9d09bbd89dea4bda315a521ece7a9a0c1b62dc72a93b6768 | MATLAB | 1,681 | 58 | function [ probs ] = AssociationLDA4( WP , BETA , W1 , pz )
%% Function WriteTopics
%
% works on single samples as well as multiple samples
% TAKE THE PRIOR TOPIC PROBABILITY INTO ACCOUNT
if iscell( WP )
% we are dealing with multiple Gibbs samples. Need to average
% predictions over these samples. Note ... |
b04a96c40a774548359a305d459398740d5a477a136d9d127bb36203c9909529 | MATLAB | 1,683 | 44 | function [vatlist,FilesExist] = ea_unifiedmapping_getlattice(obj)
% Return list of VATs
numPatient = length(obj.allpatients);
vatlist = cell(numPatient,2);
FilesExist = zeros(numPatient,2); % no sense to check for mirrored here
disp('Check for 4-D niftis...')
for sub=1:numPatient
[~,subj_tag,~] = fileparts(obj.M... |
91dd15f24519a21d1d339723415612eaf5723ddbcfc35917deb4fde4f486ec54 | MATLAB | 1,684 | 50 | function tree = copy(tree,subuid,uid)
% XMLTREE/COPY Copy Method (copy a subtree in another branch)
% FORMAT tree = copy(tree,subuid,uid)
%
% tree - XMLTree object
% subuid - UID of the subtree to copy
% uid - UID of the element where the subtree must be duplicated
%_______________________________... |
058f6ac52133736c1bef5b7b30bb7a8c6ed5ea3e66307edb8d8747bd854ae461 | MATLAB | 1,685 | 43 | function h = UIcolorshift(varargin)
%UIcolorshift Creates an interactive colorbar.
% UIcolorshift adds a (vertical) colorbar to the current axes. This
% colorbar can be used to shift or rescale the color mapping in the
% current axes. Clicking near the top of the colorbar axes
% up or down (right or left... |
3819e808f2b1cb5b799ff21b5881a022a4c50cea916208c00b88bd80e34062bc | MATLAB | 1,685 | 75 | %
% Copyright (c) 2015, Yarpiz (www.yarpiz.com)
% All rights reserved. Please read the "license.txt" for license terms.
%
% Project Code: YPML110
% Project Title: Implementation of DBSCAN Clustering in MATLAB
% Publisher: Yarpiz (www.yarpiz.com)
%
% Developer: S. Mostapha Kalami Heris (Member of Yarpiz Team)
... |
9697cdfd3e0361f1f945ffb3e29f22bd5b3042b424a021f96cc6c4058f5f5d04 | MATLAB | 1,685 | 58 | function [res, errStr, fName]= dtdstruct_read(fName)
%
%function [res, errStr, fName]= dtdstruct_read(fName)
%
% Opens a dtdStruct from the filesystem
%
% fName: should contain the path and file name. if it is empty or undefined, a file selection dialog will appear
%
% return values:
% res: contains ... |
ea41c1c689790c0f84ae24522793890fca8d33b374e80cf8329d5f9d73f9427a | MATLAB | 1,685 | 50 | function model = fitGMM(X, options)
% Fits a GMM to a matrix of feature vectors
% X is a N x nFeatures array, each row is a single neuron's features
% requires at least options.maxK + 1 neurons
% Params
Kmax = options.maxK;
chooseK = options.chooseK;
sparseLambda = options.sparseLambda;
% If no pre-specified number o... |
4c17b2b5835418486c548cc61a4f5e2c328615837028e1dc3b3ac866b490b865 | MATLAB | 1,686 | 57 | function fcs = cfs2fcs(cfs,fs)
%CFS2FCS Calculate gammatone crossover frequencies.
%
% FCS = IOSR.BSS.CFS2FCS(CFS,FS) calculates the crossover frequencies of a
% gammatone filterbank. The output fcs is the same size as CFS, with the
% last element being equal to fs/2.
%
% The crossover frequencies are determi... |
1168adb4b06e1f7f36fccc8f58ac20abdecd601003a975ad494445b781ffce05 | MATLAB | 1,687 | 74 | function [phis, cdf, phiplot, cdfplot] = circ_samplecdf(thetas, resolution)
% [phis, cdf, phiplot, cdfplot] = circ_samplecdf(thetas, resolution)
%
% Helper function for circ_kuipertest.
% Evaluates CDF of sample in thetas.
%
% Input:
% thetas sample (in radians)
% resolution resolution at which the cdf... |
67170e11b394c974f73a1a91daf8108e90761cf562ccfbe14fa1c2679bdaebd6 | MATLAB | 1,687 | 69 | % Optimal doping profile optimization
% Boyd, Kim, Vandenberghe, and Hassibi, "A tutorial on geometric programming"
% Joshi, Boyd, and Dutton, "Optimal doping profiles via geometric programming"
% Written for CVX by Almir Mutapcic 02/08/06
% (a figure is generated)
%
% Determines the optimal doping profile that minimiz... |
a6199ad86b50434cf2144df14f81e1e53d98859f31e1f064afa825c563674e45 | MATLAB | 1,687 | 78 | function [n, ts] = nex_ts(filename, varname)
% nex_ts(filename, varname): Read timestamps from a .nex file
%
% [n, ts] = nex_ts(filename, varname)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% varname - variable name
% OUTPUT:
% n - number of timestamps
% ts - array of timestamps (in seco... |
3d0c3dca0018f722b9b7369077856569696af866c85157f42c6e493cba7f852e | MATLAB | 1,688 | 66 | % Figure 7.1: Logistic regression (GP version)
% Section 7.1.1
% Boyd & Vandenberghe, "Convex Optimization"
% Kim & Mutapcic, "Logistic regression via geometric programming"
% Written for CVX by Almir Mutapcic 02/08/06
%
% Solves the logistic regression problem re-formulated as a GP.
% The original log regression probl... |
c6ecd35eefa6698e97af9fb6611e13767e342e81b9823b8b9d30eadbe10ba646 | MATLAB | 1,689 | 49 | function myPLS_plot_loadings_2D(var,var_name,signif_LC,pos_threshold,neg_threshold,save_opts)
%
% This function plots 2-dimensional loadings (e.g. correlation matrix)
% of all significant latent components (LCs)
%
% Inputs:
% - var : M x L matrix, M is #imaging values (when vectorized),
% ... |
f10be76c7653303bbebe39df80dd27d0da9e52e864824f7f23a77d0e404cdf04 | MATLAB | 1,689 | 54 | function plotAreaGMMCompPDFs(allROIs, areaGMM, cmap)
% Creates KDE plots for all metric value distributions separated by
% components within an area-specific GMM
% Check size matches
nComponents = areaGMM.model.NumComponents;
assert(nComponents == size(cmap,1))
% Params
metricFields = {'duration', 'sharpness', 'linea... |
3632e274ea35549aa9ef1eecbaa123826137d44e8500d9e02cbfaee843a888a6 | MATLAB | 1,690 | 65 | function ea_surfice(script, hold)
% Wrapper for Surf-Ice script call
if ~exist('hold', 'var')
hold = 1; % Block executions until script QUIT
end
% check OpenGL version
% openglInfo = opengl('data');
% openglVer = strrep(regexp(openglInfo.Version, '(^[\d.]+)(?=.*)', 'match', 'once'), '.', '');
% if numel(openglVer... |
836bb21dc6171945ae44cb2b88ed635e7bfa76ba9ed5f6a60f5bf0f7c111856f | MATLAB | 1,690 | 67 | %%*******************************************************
%% Doptdesign: D-optimal experiment design.
%%
%% max log(det(sum_{i=1}^p lambda_i v_i v_i^T)) + const
%%
%% s.t. lambda_i >= 0, sum_{i=1}^p lambda_i = 1.
%%
%% Note: const = n.
%% V: nxp matrix with n <= p.
%% lambda: lambda_i is the fractio... |
aff8c80a568b340f3bf8fe063bc7f67c74bf467531597ad8916dff89af608ef7 | MATLAB | 1,690 | 59 | %islvector - Test if parameter is a (pseudo) logical vector satisfying an optional list of tests.
%
% USAGE
%
% test = islvector(x,test1,test2,...)
%
% x parameter to test
% test1... optional list of additional tests (see examples below)
%
% EXAMPLES
%
% % Test if x is a logical vector
... |
690605436ca14850c6846a915a69af1beff944076f62257ca2adf56ed7ba0a25 | MATLAB | 1,691 | 58 | function [Theta] = tikhonov_MetaInfer(rp,X,F_prime)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically relevant behaviors of the ecosystems.
% Copyright (C) 2015 Vanni B... |
2063c61e3512a958c7af1459787ab387db5106bbf4fcdd83b909d61c12163e2d | MATLAB | 1,692 | 47 | % r = getRadAvg(im)
% ---------------------------------------
%
% Return the radial average of input square image im
%
% Inputs:
% im Square image
%
% Outputs:
% r Radial average
%
% ---------------------------------------
%
% A detailled description of the method can be found in :
% "Descloux, A., K... |
2d75d298d7bbfdbdbb45e205fd149b09d1d31d2eb25a1563ef8dc48c9ae73bb8 | MATLAB | 1,692 | 39 | function [bins,binNames] = discretize(inputData,edges)
%DISCRETIZE Create a categorical array by discretizing numeric data.
% BINS = DISCRETIZE(A,EDGES) returns the bin numbers obtained by discretizing
% the numeric array A into categories. EDGES is a numeric vector that
% contains bin edges defining the categor... |
d74c3234505f16f0bfcec5e1d212a1bbb930dbf73e427e2db25f792e9e766248 | MATLAB | 1,692 | 51 | function [q, X, Y, Z] = domain2vec(domain, resolution)
%DOMAIN2VEC matrix of column vectors for meshgrid points
% [q, X, Y, Z] = domain2vec(domain, resolution) returns a matrix of
% column vectors for the meshgrid point coordinates over a parallelepiped
% domain with the given resolution. The individual c... |
043bd5f7c541c19de2ded9946656a4e5d6551a2c1515a26fffcd6047f5fbfff5 | MATLAB | 1,693 | 90 | function [vertex,face] = read_vtk(filename, verbose)
% read_vtk - read data from VTK file.
%
% [vertex,face] = read_vtk(filename, verbose);
%
% 'vertex' is a 'nb.vert x 3' array specifying the position of the vertices.
% 'face' is a 'nb.face x 3' array specifying the connectivity of the mesh.
%
% Copyright (c)... |
5abebf9b11a507951a3114beccb1400b421a0fcd6700c1d57b9fccc0a8729975 | MATLAB | 1,693 | 57 | function I = shift_reconstruct(Y,shifts,diffphase,us_fac,Nr,Nc,Np,method,add_value)
% applies 3-d sub-pixel shifts to an input image
% INPUTS:
% Y: input image (double 3d tensor) in space (real) or frequency (complex) domain
% shifts: shifts
% diffphase: phase difference
% us_fac: upsampling... |
a7a68b15e7a6747e1b87ff6f34398c0bdf96ad2d289da71b724bfc399202d3a9 | MATLAB | 1,693 | 51 | % [labels, start, stop] = Boris.Tabulated.load(filename)
% Returns a list of events encoded with BORIS.
% Output:
% labels: 'behavior1', 'behavior2', ...
% start: [start1, start2, ...];
% stop: [stop1, stop2, ...]
%
% epochs = Boris.Tabulated.load(filename)
% Output:
% {'behavior1', [start1, stop1, st... |
a83a3c00f75e0999a3c67d88287c527560ab5ef7bccdd8a563ab76d659a2dac6 | MATLAB | 1,693 | 65 | function new = DBDuplicate(old,new,varargin)
%DBDuplicate - Duplicate database.
%
% USAGE
%
% name = DBDuplicate(old,new)
%
% old database to duplicate
% new new database name (see NOTE below)
%
% NOTE
%
% Database names can include wildcards to indicate current date and time:
%
% ... |
c16d65eeb46fa4555e4e35fd77e60598bd74cbdee373374d526e201e7baf781f | MATLAB | 1,693 | 54 | % Box volume maximization
% Boyd, Kim, Vandenberghe, and Hassibi, "A Tutorial on Geometric Programming"
% Written for CVX by Almir Mutapcic 02/08/06
% (a figure is generated)
%
% Maximizes volume of a box-shaped structure which has constraints
% on its total wall area, its total floor area, and which has lower
%... |
c371275b2e5310e0e56d3635d3db38feef0f45777f37e1106814f052712c4222 | MATLAB | 1,693 | 46 | function [H] = translate(T);
% TRANSLATE returns the homogenous coordinate transformation matrix
% corresponding to a translation along the x, y and z-axis
%
% Use as
% [H] = translate(T)
% where
% T [tx, ty, tz] translation along each of the axes
% H corresponding homogenous transformation matrix
% Copyrig... |
ce6dec8e58c6f4f3b1eedee7ee146a80fd9c1787770536569fc2e418716368ce | MATLAB | 1,693 | 68 | function cells = ValidCells(self)
% returns matrix 'cells', an Nx2 matrix of [Tetrode Number, Cell Number] of viable cells
% if f_min is set, the number of total spikes/total recording time (not given epoch set time) must be >f_min
% for that cell to be included
% if checkdrift~=1 && exist('checkdrift'), then the sc... |
f4fcf84d4524dcabe8931a9b047b4088eb10411dea28f3bf2d4f5d9fddec0b63 | MATLAB | 1,693 | 73 |
% This file is a demonstration of how to call gbvs()
% make some parameters
params = makeGBVSParams;
% could change params like this
params.contrastwidth = .11;
% example of itti/koch saliency map call
params.useIttiKochInsteadOfGBVS = 1;
outitti = gbvs('samplepics/1.jpg',params);
figure;
subplot(1,2,1);
imshow(imr... |
98507e43af29a8574dce81ebeb1086a9acc3cd9f1a96d216006a482bc80872c3 | MATLAB | 1,694 | 57 | function till_save_nii(vol,img)
file = vol.fname;
if contains(file,'.nii.gz')
for i=1:numel(vol)
vol(i).fname = file(1:end-3);
end
if ndims(img)<4
spm_write_vol(vol,img);
elseif ndims(img) == 4
nimg = size(img,4);
if ~isequal(vol(:).mat)
warning('4D... |
e48749e69fa3737a8e409eaa04f13b59b5fc958cf9e1b8f9dc14cd5b2167db8b | MATLAB | 1,694 | 50 | function obj=facet_wrap(obj,col,varargin)
% facet_grid Create subplots according to one factor, with wrap
%
% Example syntax (default arguments): gramm_object.facet_wrap(variable,'ncols',4,'scale','fixed')
% This is similar to faced_grid except that only one variable
% is given, and subplots are arranged by column, wit... |
ea03a3284c5c1dcce33aaf0d573d2785465c45172728f076e00a76a8f3276d17 | MATLAB | 1,694 | 58 | function [S, f] = plot_spk_spectrum(self, cel)
% plots the Frequency power spectrum for spiking
%
% Returns
% S -> spectrum
% F -> frequency vector
%
% andrew bogaard 3 april 2010
import CMBHOME.Utils.*
AddChronuxPackage;
params.Fs = 40; % set params for spect function. bin in .025s bins
params.f... |
04ca98ccdbc0d24b732d14fa0fe1ca093bbb68c937bb7842447bcd6ba86c410b | MATLAB | 1,695 | 42 | % GIfTI Class for MATLAB
%
% Geometry format under the Neuroimaging Informatics Technology Initiative
% (NIfTI):
% http://www.nitrc.org/projects/gifti/
% http://nifti.nimh.nih.gov/
%
% This MATLAB class is part of SPM:
% https://www.fil.ion.ucl.ac.uk/spm/
%
% It rel... |
f8f0a5e06b4dad771f56616dd9b3e17967a27bad0db7029abc1ad9ec1a62c5ea | MATLAB | 1,696 | 70 | function [h mu ul ll] = circ_mtest(alpha, dir, xi, w, d)
%
% [pval, z] = circ_mtest(alpha, dir, w, d)
% One-Sample test for the mean angle.
% H0: the population has mean dir.
% HA: the population has not mean dir.
%
% Note: This is the equvivalent to a one-sample t-test with specified
% mean direction.
... |
ffd25699597cb3e3dbd85f320506249154bf337e02954608dfed7937fe8d6039 | MATLAB | 1,696 | 62 | % Maximum volume inscribed ellipsoid in a polyhedron
% Section 8.4.1, Boyd & Vandenberghe "Convex Optimization"
% Original version by Lieven Vandenberghe
% Updated for CVX by Almir Mutapcic - Jan 2006
% (a figure is generated)
%
% We find the ellipsoid E of maximum volume that lies inside of
% a polyhedra C described ... |
5952aa37b891b46133bc16dfd809c6aa48017aebebde1a61d6b5b6cb023a0b2f | MATLAB | 1,697 | 77 | function dout=getSpectroEnv(data,t,wt,wr,wot,fs)
% Usage ... y=getSpectroEnv(x,t,ww_twid,ww_franges,ww_tskip,fs)
%
% data, time (t) for data, wt (window width in time),
% wr (frequency ranges), wot (window skip time), fs (sampling freq),
if ~exist('fs'), fs=1/mean(diff(t)); end;
if ~exist('wot'), wot=1/fs; en... |
88bef8f8a88da6865d230d51a8d510668e9bace60990640c61c832aaf27d5274 | MATLAB | 1,697 | 49 | function Z = zstream(action,D)
% Compress/decompress stream of bytes using Deflate/Inflate
% FORMAT Z = zstream('C',D)
% D - data stream to compress (converted to uint8 if needed)
% Z - compressed data stream (uint8 vector)
% FORMAT D = zstream('D',Z)
% Z - data stream to decompress (uint8 vector)
... |
8c7e0072de9663a01d7f7b6751f1a2e592fbc002acf6632e03dfedd412ec5e14 | MATLAB | 1,697 | 45 | function sout = cvx_power_warning( flag )
%CVX_POWER_WARNING Controls the CVX warning message for x.^p expressions.
% CVX converts power functions like x.^p, for variable x and fixed p, into
% solvable form using an SOCP transformation. For quadratics x.^2 and square
% roots x.^(1/2), a single second-orde... |
b8810a09c76060bd34c1bafe7caa091b903debd5f4d720f707fdedb4ffb77d72 | MATLAB | 1,697 | 48 | % kurt() - return kurtosis of input data distribution
%
% Usage:
% >> k=kurt(data)
%
% Algorithm:
% Calculates kurtosis or normalized 4th moment of an input data vector
% Given a matrix, returns a row vector giving the kurtosis' of the columns
% (Ref: "Numerical Recipes," p. 612)
%
% Author: Martin Mckeown, CNL... |
4b42b161af8a8348ee52be7c1e702ec7acb801cc7655bd3265931bbe0c50a537 | MATLAB | 1,698 | 32 | function [tapers,eigs]=dpsschk(tapers,N,Fs)
% Helper function to calculate tapers and, if precalculated tapers are supplied,
% to check that they (the precalculated tapers) the same length in time as
% the time series being studied. The length of the time series is specified
% as the second input argument N. Thus ... |
b06f43ac1abfe6eb7195c6ba7891efadd08c0b7987f60849884bdc438eca0f88 | MATLAB | 1,698 | 41 | function [upcovar,upmu] = updatecov(data,covar,mu,addrow,delrow,option)
% This function updates the mean and covariance matrix of the full data
% after adding or removing observations.
%
% Input arguments:
% data : the original data
% covar : the covariance matrix of the data
% ... |
9210afdd96a08e580f748a593b47cf716f6f0829a40a1c50c5a6599f4af6fd3c | MATLAB | 1,699 | 67 | function scenario = scenario_QAr_Qb_sump(par)
% r(Q,A), b(Q), p(Q+A,Q+A)
scenario.name = "QAr_Qb_sump";
% define parameter set (names)
scenario.parnames = {'r0','K','b0','beta','p0','H'};
% organize parameters in structure form
scenario.make_par = @(p) struct( ...
'r0', p(1), ...
'K', p(2), ...... |
13ff70ceea67c0c8dc020f6a6564c007789e88abab5ed13731a5318d4364421e | MATLAB | 1,700 | 42 | function Ad = adendotd(dense, d, sparAd, Ablk, blkstart) %#ok
% Ad = Adendotd(dense, d, sparAd, Ablk, blkstart)
%
% ADENDOTD Computes d[k]'*Aj[k] for Lorentz blocks that are to be factored
% by dpr1fact.
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 by I... |
24ebad8d1872f1889fe9e9d8343917cb86a6a34ff1b058a7740e8b3b8ce77791 | MATLAB | 1,700 | 49 | %% Point3D - object representing a Point in 3D spaec
% "no frills" Version
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
classdef Point3D < plotable3D & han... |
9196da108a9a28d5d4836726c5e1ba8311fff7f767da42f74153322d6a4d233e | MATLAB | 1,700 | 64 |
function [ks_t0, ks_t1, anim_windows_sec] = restrict_time_drift(animal, shank, ks_times, tracks, metadata_dir)
%all outputs in seconds
load([metadata_dir '\ChannelSetsByTrack_forSpikes_V2']); %load file containing time window information
%load(['F:\Ephys Analysis\ChannelSetsByTrack_forSpikes_V2']);
%removed a... |
c022a640e16bb00e3d72f919b4f11c32929c1df40bb3a00a827e0d3c85b7934c | MATLAB | 1,700 | 41 | function y = qblkmul(mu,d,blkstart) %#ok
% y = qblkmul(mu,d,blkstart)
%
% QBLKMUL yields length(y)=blkstart(end)-blkstart(1) vector with
% y[k] = mu(k) * d[k]; the blocks d[k] are partitioned by blkstart.
%
% ********** INTERNAL FUNCTION OF SEDUMI **********
%
% See also sedumi
% This file is part of SeDuMi 1.1 b... |
42a63c197cda5d3b9b185cb0ba0518ca1655e27a506461cb9e24abd01bf40f6a | MATLAB | 1,701 | 43 | function data_out = importvelocity(filename, dataLines)
%IMPORTFILE Import data from a text file
% M001HBASELINE1VELOCITY = IMPORTFILE(FILENAME) reads data from text
% file FILENAME for the default selection. Returns the data as a table.
%
% M001HBASELINE1VELOCITY = IMPORTFILE(FILE, DATALINES) reads data for
... |
8fdf47bbaec95b50d8f1e8da6fd0f3f6ccaf3f35522018bb4ed92442a1ad4ed1 | MATLAB | 1,701 | 30 | %% qMetric to parquet
% For now, create only one parquet files and keep matlab struct for the GUI
yourQMetricFile = dir('/home/netshare/zinu/JF070/2022-06-13/ephys/site1/qMetrics/qMetric.mat');
load([yourQMetricFile.folder filesep yourQMetricFile.name])
qMetricSummary = table('Size',[length(qMetric.clusterID), 10],... |
c5a9b02c17704f5e6d3445d24cec8e50b670ee3afe3df588d619b93ad264cbdb | MATLAB | 1,702 | 58 | function [R P b] = plot_velocityrate(self, cel, params)
% Plots firing rate as a function of running speed (pre2016)
%
% root.plot_velocityrate(cel)
% root.plot_velocityrate(cel, params)
%
% Plots the firing frequency of cell cel against animal running speed for
% root.epoch (if multiple, they are all concatinated. Se... |
0e2b9a7dc65f811302e39c68514aeaefafd1100880fe42f332e670b9a2144b92 | MATLAB | 1,703 | 47 | function warnUnknownOptions(opts, known, pipelineName)
% warnUnknownOptions Warn about opts fields the pipeline will silently ignore.
%
% warnUnknownOptions(opts, known, pipelineName)
%
% MATLAB struct field names are case-sensitive, so a misspelling such as
% opts.nrepeats when the pipeline reads opts.nRepeats ... |
65d5bc8b66f9d2e1c082d11cab4e547a59f85bc99dc8d675248a46d406ca7626 | MATLAB | 1,703 | 48 | function [H] = scale(S);
% SCALE returns the homogenous coordinate transformation matrix
% corresponding to a scaling along the x, y and z-axis
%
% Use as
% [H] = translate(S)
% where
% S [sx, sy, sz] scaling along each of the axes
% H corresponding homogenous transformation matrix
% Copyright (C) 2000-2005,... |
83476e6e677b609f0f934fd3d85be87db4302f3f7b3b74a10f8979cd181ae070 | MATLAB | 1,703 | 50 | %%*******************************************************************
%% HKMdirfun: compute (dX,dZ), given dy, for the HKM direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*******************************************************************... |
0135e6bf2dddca6026b6b63132743f56ccfd842f7669765761a4f9cba74288ec | MATLAB | 1,704 | 55 | function ea_autocrop(input, output, opts)
% Crop the image to its minimum bounding box
arguments
input {mustBeFile}
output {mustBeTextScalar} = '' % Overwrite input by default
opts.mask {mustBeNumericOrLogical} = false % Do not mask the image (remove background) by default
opts.margin {must... |
0a398db32dfa3405dc551465e234560ae5c71289e8332db44801932dce724824 | MATLAB | 1,704 | 50 | % eeg_getica() - get ICA component activation. Recompute if necessary.
%
% >> mergelocs = eeg_getica(EEG, comp);
%
% Inputs:
% EEG - EEGLAB dataset structure
% comp - component index
%
% Output:
% icaact - ICA component activity
%
% Author: Arnaud Delorme, 2006
% Copyright (C) Arnaud Delorme, CER... |
122c7dd0e9ef5865f88f81927bdbe3524e12f814a9f60b94bcb7bb7c09050bc5 | MATLAB | 1,704 | 62 | function r = circ_r(alpha, w, d, dim)
% r = circ_r(alpha, w, d)
% Computes mean resultant vector length for circular data.
%
% Input:
% alpha sample of angles in radians
% [w number of incidences in case of binned angle data]
% [d spacing of bin centers for binned data, if supplied
% ... |
1c764aed2d986753d4a7e637aa7fbb9dba7e244f9a52290a6a27a28c93b28543 | MATLAB | 1,704 | 48 | %% Frequency band segment
% fRanges{1, 1} = [1.8, 2.2]; % prediction
% fRanges{2, 1} = [0.6, 4.4]; % delta
% fRanges{3, 1} = [4.6, 7.6]; % theta
% fRanges{4, 1} = [8.1, 13.2]; % alpha
% fRanges{5, 1} = [14.1, 32.5]; % beta
% fRanges{6, 1} = [34.9, 69.8]; % gamma
% fBands = {'prediction', '\delta', '\theta', '\alpha', '... |
8fe3248a21d47511881a087170c7e227ab678b56e8fcaaf40d47c63697fc55cc | MATLAB | 1,704 | 50 | function data=ea_readUI(UI)
%readUI Attempt to read a user input.
%
% DATA = readUI(UI) reads a user input described in UI and returns the
% relevant data. An empty array is returned if UI could not be read.
%
% Remark:
% Attempts to read UI are made in the following order:
% 1. Binary ma... |
37f75b32d6c3d3544c5a3a15c1d15a05850d803d8e7bb21f372e17ca5b1654ff | MATLAB | 1,705 | 67 | function scenario = scenario_Qsumr_Qb_sump(par)
% r(Q,Q+A), b(Q), p(Q+A,Q+A)
scenario.name = "Qsumr_Qb_sump";
% define parameter set (names)
scenario.parnames = {'r0','K','b0','beta','p0','H'};
% organize parameters in structure form
scenario.make_par = @(p) struct( ...
'r0', p(1), ...
'K', p(2... |
a6d86903d569f8829d428113fdf21e6052c14d20456f72e57d8af5cc239d58cd | MATLAB | 1,705 | 65 | %% RDIR Enhanced - Examples of use
%
% This script demonstrates how to use the different abilities of the
% enhanced |rdir| function.
%
% Examples are based on |matlabroot| directory content. Results may vary
% depending on your version of Matlab.
%
%% Standard use
rdir([matlabroot, '\*.txt'])
%% Using double wildcar... |
3d4a6181ccdc291c1d87ca5bfcf63410648dcab7ffd1295f9116512fe0837631 | MATLAB | 1,707 | 50 | function [data,indices] = GetSpikeFeatures(group)
%GetSpikeFeatures - Get spike features.
%
% USAGE
%
% features = GetSpikeFeatures(group)
%
% group electrode group
%
% OUTPUT
%
% features (timestamp,group,cluster,features...) t-uples.
%
% NOTE
%
% Contrary to e.g. GetSpikes, this functio... |
d3b8a39b3bfac8947151a13a2a99f9c86dff8d1d14c8b715abaa41ba66e4bd69 | MATLAB | 1,707 | 55 | function cvx_optpnt = exponential( sx )
%EXPONENTIAL Exponential cone.
% EXPONENTIAL, called with no arguments, creates three scalar variables X,
% Y, and Z and constraints them to lie in an exponetial cone. That is,
% given the declaration
% variables x y z
% {x,y,z} == exp_cone
% constraints th... |
374d41bbdeb4418b345c1d4daffcac5c049f006bee27896a91806a27f2dc89dc | MATLAB | 1,708 | 65 | function p = editParamStruct(p)
fignum = figure('NumberTitle','off',...
'Menubar','none',...
'Toolbar','none',...
'Name', 'Edit Parameters');
clf;
pos = get(fignum,'position');
fnames = fieldnames(p);
thei = -[0... |
a862eb4ac9219b74ea10626b98da73f89005222a987f8c44e7bd4c987a5bcdef | MATLAB | 1,708 | 58 | function write_off(filename, pnt, plc)
% WRITE_OFF writes a set of geometrical planar forms (called piecewise linear complex, PLC)
% to an ascii *.off file, which is a file format created by Princeton Shape Benchmark
%
% Use as
% write_stl(filename, pnt, tri)
%
% See also READ_OFF
% Copyright (C) 2010, Cristiano Mi... |
52880f5311365292c7dfb8f0f23a6b526c52eb2dbae8192e9f3b43d2aa0ad503 | MATLAB | 1,710 | 62 | function r = circ_r(alpha, w, d, dim)
% r = circ_r(alpha, w, d)
% Computes mean resultant vector length for circular data.
%
% Input:
% alpha sample of angles in radians
% [w number of incidences in case of binned angle data]
% [d spacing of bin centers for binned data, if supplied
% ... |
16dc1f54b0113abc3367dda78109c0f3a40fe6a2c75e95323f211c89694d72d9 | MATLAB | 1,711 | 34 | %% Place field rate map
n_bin_maze = 100; % number of spatial bins
c_L_bin = c_L_path/n_bin_maze; % bin size
c_sigma = 3; % Gaussian kernel width (in bins)
c_kernel_G = normpdf(-ceil(3*c_sigma):ceil(3*c_sigma),0,c_sigma) ...
/ sum(normpdf(-ceil(3*c_sigma):ceil(3*c_sigma)... |
76bbb7be0538fca982a521d3688f9881e902b3aa7d437f20f939ab6bcd4a0135 | MATLAB | 1,711 | 40 | function vatlist = ea_sweetspot_getvats(obj)
% Return list of VATs
numPatient = length(obj.allpatients);
vatlist = cell(numPatient*2,2);
modelLabel = ea_simModel2Label(obj.M.vatmodel);
disp('Construct VAT list...')
for sub=1:numPatient
% Original VAT E-field
stimFolder = [obj.allpatients{sub}, filesep, 'stim... |
bf19103201eb63546cf00a89c6028aef77b0de47aaf71b35406a057f37a887f8 | MATLAB | 1,711 | 62 | function [returnVar,msg] = RemoveDCfromDat(fname,nbChan)
% USAGE:
% RemoveDCfromDat(fbasename,nbChan)
% This function removes DC from dat files by computing the average of
% the first 1e6 samples (or less if file is smaller)
% INPUTS:
% fname: dat file name
% nbChan: total number of channel... |
2f0dc8cbb8e9bc32dd7bf1f0a0108ee338987349f55c7b719dd0a1b6892186ed | MATLAB | 1,712 | 49 | function Z_flip = CBIG_MMLDA_behavior_to_zscore(behavior, regressor, behavior_sign, refpara)
% Z_flip = CBIG_MMLDA_behavior_to_zscore(behavior, regressor, refpara)
%
% Convert behavior matrix to zscore with respect to reference cohort.
% 1. Regress out regressors with respect to reference.
% 2. Zscore withe respect ot ... |
8a3ce581f298a2e9a121734056242ca782ce87a1a1311d00a4e7e91401c72775 | MATLAB | 1,712 | 40 | function vatlist = ea_unified_ss_getvats(obj)
% Return list of VATs
numPatient = length(obj.allpatients);
vatlist = cell(numPatient*2,2);
modelLabel = ea_simModel2Label(obj.M.vatmodel);
disp('Construct VAT list...')
for sub=1:numPatient
% Original VAT E-field
stimFolder = [obj.allpatients{sub}, filesep, 'sti... |
48768f40eda38e1f0bf5f5de31d37a27c8277a45d60f6c10d127b9adf3beef96 | MATLAB | 1,713 | 54 | function [x,phi,a,phi_knot,rho_c,p] = corrC2L(x,phi)
% Find the linear correlation between a linear and circular variable as in
% R. Kempter 2012, Journal of Neuroscience Methods.
%
% Inputs: x - the linear variable
% phi - circular variable (must be in radians)
%
% Output: x - Same as the input l... |
88df680451ab4d512f2d88cccf9249a1f605f9060c44427687f4c92b3567dc61 | MATLAB | 1,713 | 68 | function scenario = scenario_sumr_sumb_sump(par)
% r(Q+A,Q+A), b(Q+A), p(Q+A,Q+A)
scenario.name = "sumr_sumb_sump";
% define parameter set (names)
scenario.parnames = {'r0','K','b0','beta','p0','H'};
% organize parameters in structure form
scenario.make_par = @(p) struct( ...
'r0', p(1), ...
'K', ... |
1182a0a1844d4c9c649787b186bd4371adfccfa602ad183c347671b8bd45a97d | MATLAB | 1,714 | 58 | % SPLITBY split a string while respecting grouping
%
% SPLITBY(str, '.', {'"', '[]'}) splits `str` on each period which is
% not enclosed in square brackets or double quotes.
function parsed = splitby(str, to_split_by, to_respect)
% make convenient structure out of delimiter arguments
delims = cellfun(@delim_d... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.