sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c6fd2b7171de3a712cffa79502e025526a1386eb0e2252d356d9cc7c427d59a9 | MATLAB | 1,059 | 34 | function [subj] = remove_mat(subj,objtype,objname)
% Sets the mat field of the OBJNAME of OBJTYPE to empty.
%
% [SUBJ] = REMOVE_MAT(SUBJ,OBJTYPE,OBJNAME)
%
% N.B. This doesn't change the subj.x strings. If subj.x refers to
% the object that was just removed, remember to update subj.x
% accordingly.
% License:
%======... |
546a1625ec60a55f15f979ebfc9d27c598d7c32d04fedebd960344f273307c0c | MATLAB | 1,060 | 42 | function [y] = create_legendre(timepoints, N, norm)
% Generates legendre polynomials of specified order.
%
% Usage:
%
% [Y] = CREATE_LEGENDRE(N, POLORT)
% [Y] = CREATE_LEGENDRE(N, POLORT, NORM)
%
% Generates legendre polynomials of order up to POLORT with norm NORM
% (default NORM 'unnorm'). Spaces the polynomial ac... |
5581fe4762106fb6f1ffd7f01395acf3d6f3dc6755d96f38d2bafdb003ba20c8 | MATLAB | 1,060 | 33 | function [z, sd, m] = cellzscore(x, dim, flag)
% [Z, SD] = CELLZSCORE(X, DIM, FLAG) computes the zscore, across all cells in x along
% the dimension dim, normalising by the total number of samples
%
% X should be an linear cell-array of matrices for which the size in at
% least one of the dimensions should be the ... |
9a4fd0750e7f22f2e0b97d9156a72acf5b1b97307d469070c0e253a4c5868973 | MATLAB | 1,060 | 26 | % shuffle local features function
% October 26 2022
% Amirhossein Farzmahdi
function [insertion_images, fc6_selected_units_ins_res_image] = insertion_feature(nview,selected_percent,img_size,bckg,sum_maps,images,net,layer,unit)
for i_view = 1:nview
one_pixel = find(sum_maps{i_view}(:));
[~, sort_ind] = sort(ab... |
b60ed8fde915c5fecd09c59a49e3bf0e4e1c987aeaf4c7e16efc5545ebdb77b5 | MATLAB | 1,060 | 23 | % function output = transres_rsa_beta(decoding_out, chancelevel, varargin)
%
% Calculate a GLM using cfg.files.components.matrix as regressors and
% decoding_out(cfg.design.components.index) as data. The resulting betas are
% returned as output. For multiple calculations, these are faster when the
% inverse of cfg.des... |
2be78008bcf57e3de0b8383281bab5a3142846a0706dfc68147d408c4ed66b8a | MATLAB | 1,063 | 34 | function [status,txt] = scp(cmd, isRunAsync)
% USAGE:
% [status,txt] = scp([cmd, isRunAsync])
% INPUTS:
% - If no inputs provided will return true or false indicating, is scp
% installed on this computer.
% - cmd - scp command to run.
% - isRunAsync - when set to true will execute scp command and ret... |
5d6094c4ad3e661fff8d27a93ada0fe99493ae235bc3383d63f8a5cad0b8da83 | MATLAB | 1,063 | 37 | function [subj] = change_objgroup(subj,objtype,objnames,new_group_name)
% Change group name of multiple objects at a time
%
% [SUBJ] = CHANGE_OBJGROUP(SUBJ,OBJTYPE,OBJNAMES,NEW_GROUP_NAME)
%
% This goes through each object in OBJNAMES, changing their
% GROUP_NAME to NEW_GROUP_NAME
%
% OBJNAMES is a cell array of objec... |
d8b62a98c410824f7a3ddbb087d4cb0f08822795bdead5a04effe6cc7286c594 | MATLAB | 1,063 | 50 | function circleColor(M, x, y, cmap)
if nargin < 5
Mcol = M;
end
if length(x) ~= size(M, 2) | length(y) ~= size(M,1)
error('x and y should have the same length as dimensions of M');
end
n = 100;
l = linspace(0, 2*pi, n);
th = linspace(0, 2*pi, n);
r = 1;
... |
b42d9d534b841350d55eabe106aef9a205e923a5a64faff85974f82e3e3ac5e1 | MATLAB | 1,064 | 29 | function angle_degrees = angle_between_vectors(vector1, vector2, type)
if nargin == 2
type = 'cosine';
end
% Calculate the dot product of the two vectors
switch type
case 'cosine'
dot_product = dot(vector1, vector2);
% Calculate the norms of ... |
238f228b825a08652169e50655c20518197065a5638c7f6258997d1f6d86f564 | MATLAB | 1,066 | 39 | % X = vspharm(theta,phi,l,m)
%
% Vector spherical harmonic funtion (Arfken, p. 708) for quantum
% numbers l and m. Angles theta and phi should be given in radians.
% First component of X is the e_theta component and the second
% component is the e_phi component.
%
function X = vspharm_AO(theta,phi,l,m)
scale = -1/sqrt... |
0feb02f3edbef6c709b69a5bb8c595541e8a76ac5b84b6e68b8046d3db2b83da | MATLAB | 1,067 | 36 | function [g, gdata, gprior] = glmgrad(net, x, t)
%GLMGRAD Evaluate gradient of error function for generalized linear model.
%
% Description
% G = GLMGRAD(NET, X, T) takes a generalized linear model data
% structure NET together with a matrix X of input vectors and a matrix
% T of target vectors, and evaluates the grad... |
5bc4365a0d1a94d1299d4a91fee12aa397bd6d6e4acd4bc94e5b8231435f1263 | MATLAB | 1,068 | 39 | function vviq = vviq_load(p)
% function vviq = vviq_load(p)
%
% Load data of the Vividness of Visual Imagery Questionnaire (Marks, 1975)
% used for recruitment for all participnats that met the inclusion
% criteria (i.e. the recruitment pool).
%
% Output:
% - vviq: Table of questionnaire data.
%
% Simon Weber, swebe... |
9927841bd63b11f5603180879ec872bc49208415ab526a7e43a73a7ee269227c | MATLAB | 1,068 | 25 | function model = similarity_train(labels_train,data_train,cfg)
% This function passes the data for calculations of similarity carried out
% in similarity_test.
switch lower(cfg.decoding.method)
case 'classification'
% do nothing except return an data and labels as model
model.vectors... |
795dd3957f10842f1b7153eb01d14482af7221d5b6bb621ef16ada00e52a7877 | MATLAB | 1,069 | 45 | function [mdt, n_missing] = median_dt(tsa, TimeUnits)
% Find the median value of inter-event interval
%
% USAGE:
% [mdt [, n_missing] ] = median_dt(tsa)
%
% Intended for tsd that are sampled at regular intervals, this function
% returns the mean inter-event interval.
%
% INPUTS:
% tsa - a ts... |
48998ae4a94d980a2a54ddb3eb76bbaf158fd2d85bc08e4993846acb06a1521a | MATLAB | 1,070 | 31 | function create_schaefer1000_gifti(schaefer1000vector,name)
% script to create schaefer1000 gifti files for rendering
% schaefer1000vector is a 1x1000 vector with a value for each schaefer1000 region
% name is the base name of the output file (without .func.gii)
base='/Volumes/LASA/TBI_OpenNeuro/Shared_code/Turbulen... |
9c9f922b60cb929201d10f31991156cf57ea33d7a9523b9358a38bba6258e920 | MATLAB | 1,071 | 45 | function wcoef = FWT_PO(x,L,qmf)
% FWT_PO -- Forward Wavelet Transform (periodized, orthogonal)
% Usage
% wc = FWT_PO(x,L,qmf)
% Inputs
% x 1-d signal; length(x) = 2^J
% L Coarsest Level of V_0; L << J
% qmf quadrature mirror filter (orthonormal)
% Outputs
% wc 1-d wavelet transform of x.
%... |
9bd443b1317945b733f30b18608714a8aeadfda73e1f93a435175a18724657dc | MATLAB | 1,072 | 44 | function [Merge_Trajs] = Merge_AnyTraj(Traj1, Traj2)
%This will merge all of the trajectories into one cell array
%ordered cell array of every trajectory
numTraj1=size(Traj1,1);
numTraj2=size(Traj2,1);
nTraj=numTraj1 + numTraj2;
Merge_Trajs=cell(nTraj); %make an empty cell array the length of
%go throug... |
04d3bfa388d93025712caa927a70bcf90a9475ca53de9e44e7c38c31e58f089d | MATLAB | 1,073 | 26 |
if isempty(tracks)
return;
end
invisibleForTooLong = 20;
ageThreshold = 10;
% Compute the fraction of the track's age for which it was visible.
ages = [tracks(:).age];
totalVisibleCounts = [tracks(:).totalVisibleCount];
visibility = totalVis... |
a80fe547c044241f2a459b1124f298d3c3185f51881349427ad0fea917122bc7 | MATLAB | 1,073 | 29 | % Create histogram of firing rates from combined distributions.
% Plot using custom bin width.
% d1, d2, etc. are distributions of firing rates.
bin_width = 0.4;%0.4;%0.43;%0.4;%0.3;%0.3;%0.4;%0.5;%11;
fr_data3;
%dc=[d1,d1,d1,d1,d1,d1,d1,d2,d3,d3,d3,d3,d3,d3,d4,d4,d4,d5,d5,d5,d5,d5,d5,d6,d6,d6]; % combined distributi... |
ca54a313944be12b046da764d85a746fb8d25b3e46fb287f3afeac7d2f05a095 | MATLAB | 1,073 | 29 | function [y, extra, invhess] = netevfwd(w, net, x, t, x_test, invhess)
%NETEVFWD Generic forward propagation with evidence for network
%
% Description
% [Y, EXTRA] = NETEVFWD(W, NET, X, T, X_TEST) takes a network data
% structure NET together with the input X and target T training data
% and input test data X_TEST. It... |
ce2e22114038b8ee691e94053b3b1d816be1d19fbe05b7d3badc6680e1bf18de | MATLAB | 1,074 | 60 | % Compare Rprop to fminunc
%
% Copyright (c) 2012 Roberto Calandra
% $Revision: 0.55 $
%% Init
funcgrad = @onehump;
minfunc = 10e-6;
niter = 10;
p.verbosity = 0; % Increase verbosity to print something
p.MaxIter = 10000; % Maximum number of iterations
p.d_Obj = minfunc;
p.m... |
e2a0f130e3a35bc999b2ba3cee94de496c3e6ac74bbb63af41f88e3c25c3159c | MATLAB | 1,074 | 30 | function [y, extra, invhess] = rbfevfwd(net, x, t, x_test, invhess)
%RBFEVFWD Forward propagation with evidence for RBF
%
% Description
% Y = RBFEVFWD(NET, X, T, X_TEST) takes a network data structure NET
% together with the input X and target T training data and input test
% data X_TEST. It returns the normal forward... |
16ecbf2382bd4ef06cbdb80230e855928b5c65f27be5bf44a5ca4408ba829743 | MATLAB | 1,078 | 42 | function s = plus(a,b)
% Overload of the + operator
%
% USAGE:
% s = plus(a,b)
%
% the + operaetor is defined to return a tsd with same timestamps and
% data that are the sum of the data. Returns error if timestamps of the
% two object don't coincide. One of the two operands may be a scalar
% copyrig... |
deda30af2ab80527c2141f073a4c2827e38198efd408dc0c577a650be1bf3ca4 | MATLAB | 1,078 | 36 | function [wv,g]=winvar(x,percent)
% function [wv,g]=winvar(x,percent)
% returns the winsorized variance of x as wv
% returns number of winsorized observations at each tail of sample as g
% x must be a vector
% percent must be between 0 and 100; the function winsorizes the lower and
% upper extreme g values of x, where... |
f81f080b7dcbc2efd231849c70d52ab960083628ff1ed66677056a110f71e797 | MATLAB | 1,079 | 35 | % Crossings = SchmittTrigger(Signal,UpThresh,DownThresh)
%
% finds all those points where the signal crosses UpThresh in the
% upwards direction, but only for the first time after each time
% it was below DownThresh
function Crossings = SchmittTrigger(Signal,UpThresh,DownThresh)
% this is the sort of thing that would... |
9f51131086d2701bb8bafe33bcd398023f0e2037fd8fd00429665f539fc94c85 | MATLAB | 1,080 | 31 | function [gx] = g_kToM_2modes(x,P,u,in)
% wrapper around recursive k-ToM observation function
% function [gx] = g_kToM(x,P,u,in)
% A k-ToM learner bases her decision (a=1 or a=0) upon her prediction of
% her opponent's next move, given the game payoff table.
% IN:
% - x: hidden states (see indexing in inG.indle... |
590b79e0b14667e777829d0c8c79703f0e63ed857a709a2784387da1f56559cd | MATLAB | 1,082 | 26 | function isFileInSt = findFilesInST(filePaths,st,additionalFilter)
% Auxilary function returning filePaths index which are of sections to
% search for
% INPUTS:
% filePaths - cell array of filepaths to match
% st - st structure of all sections
% additionalFilter - vector to filter. Sections will be picked o... |
083d976d9ef9aa81c3effab7eac18a696f94c3e0f8ebdb6ace0b56d715bb8c82 | MATLAB | 1,083 | 39 | function [newpat] = apply_filt(pat, varargin)
% Filter the run of a pattern.
%
% [NEWPAT] = APPLY_FILT(PAT, ...)
%
% Used in conjuction with apply_to_runs.m.
%
% Arguments:
%
% FILT (optional) the filter to be used. If none is provided, the
% default is a box filter of size 3.
% License:
%===========================... |
263b6fb12e5622e1ce29a5690c094f17424004091407ff6a937211068a057366 | MATLAB | 1,083 | 27 | function y=fCSFpulse_Raw(targetdata,targetpath,savepath,calendar,save2)
%% Save CSF pulsation metric (CSFpulse) in time course.
realtargetpath = targetpath;
realtargetdataq = targetdata;
isDir=0;
for sbjc=1:length(realtargetdataq)
dataset = realtargetdataq(sbjc).name;
cd([savepath '\' dataset]);
... |
d15d837849db4701ab5c20230a83d1505af71a8598c403db5de9b6fc2488af8a | MATLAB | 1,083 | 34 | function [clabel,dval] = test_liblinear(cf,X)
% Applies a LIBLINEAR classifier to test data and produces class labels
% and decision values.
%
% Usage:
% [labels,dval] = test_liblinear(cf,X)
%
%Parameters:
% cf - classifier. See train_liblinear
% X - [number of samples x number of features] ... |
12d423e42bdab629d74af5b43fa806d59629942783e61b7d3afd71608b13d389 | MATLAB | 1,084 | 27 | % script to run all. Can take up to 2-4 hours.
% Preprocess nirs data for Figure 3, 4, 7 and 8.
prompt = 'Warning. It'' take 1-3 days to run the whole thing. Are you sure? (Y/N)';
x = input(prompt);
if strcmp(x,'Y')
sbjList = {'12','13','14','15','16','19','21','22','23','24','25'};
rawDir = 'C:\Users\m... |
934b1fa5285c6a87a0d924920a0bff6063195a281b318a32ef92faa1d588bcd2 | MATLAB | 1,084 | 35 | function [dprime logp] = dprimestats(true_labels,predicted_labels)
labels = unique(true_labels);
if numel(labels)~=2
error('Number of labels must be 2.')
end
hits = predicted_labels == labels(1) & true_labels == labels(1);
misses = predicted_labels == labels(2) & true_labels == labels(1);
false_alarms ... |
717e1acd0f1ca9abd6abe37722d4f29088ba1774a5b1bd0f1b2149be72a5a3ae | MATLAB | 1,086 | 37 | function varargout = DefaultArgs(Args, DefArgs)
% auxillary function to replace argument check in the beginning and def. args assigment
% sets the absent or empty values of the Args (cell array, usually varargin)
% to their default values from the cell array DefArgs.
% Output should contain the actuall names of argume... |
acb8727e645219fb97f62f0a89a9bfbb29899d28f48efe9dc1e5aac60710d3ff | MATLAB | 1,086 | 52 | function O = units(inp, varargin)
% O = units(quantity, unit) constructor for unit
%
% quantity is the physical quantity measured by unit (e.g. time, length)
% and unit is the unit of meaasure
% copyright (c) 2004 Francesco P. Battaglia ?M Odified by A Peyrache, 2014
% This software is released under the GNU GPL
%... |
27b0d6273c3eac761550048ff265a10a3d3da873ca11cd2bd5b2075b9cc7f62a | MATLAB | 1,089 | 35 | function [vectorField] = backward(vectorField)
% BACKWARD Flips the direction of a given vector field
%
% [vectorField] = backward(vectorField)
%
% INPUT ARGUMENTS
% vectorField - Vector field to flip
%
% OPTIONAL INPUT ARGUMENTS
% N/A
%
% OUTPUT ARGUMENTS
% vectorField - Flipped vector field
% Copyright (c) 2012 Da... |
737b18a035ccae831031d10f7561a3e466cad72ed806433ee828500d897156b8 | MATLAB | 1,090 | 40 | function [planeCoeff, normalVector] = fitPlaneAndPlot_2(points)
% At least 3 points
if size(points, 1) < 3 || size(points, 2) ~= 3
error('Deve essere fornito un array con almeno 3 punti e dimensione Nx3.');
end
% Get coordinates x, y, z
x = points(:, 1);
y = points(:, 2);
z... |
85bcfc06b8c0482daed9c81a38ffad0eb8d2f7fc59fc3bf91d86bcd43987f27b | MATLAB | 1,090 | 32 | function [SimRes] = doModel(KSD,tt,W,baseTime,modelTime,thrs,SortedStim,NDTimes)
% project to PC
PCs = projectPC(KSD,W);
% calculate crossing time
[CrossTime] = calcCrossing(PCs,tt,baseTime,modelTime,thrs);
% crossing time -> respDelay (add non-decision time)
respWin = 1; offset = 1;
... |
c7d0b93f99b0dde1125e266f2c31501b2e64d33dbf995f61e3f90c16d25d0d91 | MATLAB | 1,092 | 39 | function [ssmp] = sum(x, dim)
% [S] = SUM(X, DIM) computes the sum, across all cells in x along
% the dimension dim.
%
% X should be an linear cell-array of matrices for which the size in at
% least one of the dimensions should be the same for all cells
D = checkinput(x);
if nargin==1
dim = find(D,1,'last');
el... |
a60b6a4209f3a8009a7c19e617c93e3030b6e7dccf342a4acf46adfe385f745f | MATLAB | 1,093 | 30 | function msBatchAlignmentFFT(dirName,plotting)
%MSBATCHALIGNMENT Summary of this function goes here
% Detailed explanation goes here
%--------- Alignment parameters ----
dataFolders = msBatchFindDataFolders(dirName,[]);
for folderNum = 1:length(dataFolders)
currentFolder = dataFolders{folde... |
fda045c9b85563923e0dab45405402b5e9a660e1dc7a34a297fa607010b32114 | MATLAB | 1,093 | 45 | function [is_pos,max_r,save_fig]=seed_tunnels_with_direction_220321(source,target,fs)
% This function uses xcorr to determine the direction of spike lags to
% determine if a well is ff or fb from a tunnel. This is used if a tunnel
% cannot be determined from NMI but an electrode is still active. This is
% to be used so... |
263548f9e419f2c846ba88721af2509e58e338653f5bc225b6f60b1baa210d88 | MATLAB | 1,095 | 44 | function modules = parseGitSubmodulesFile(repo)
modules = cell(0,3);
if ~exist('repo','var') || isempty(repo)
repo = [pwd, '/'];
end
currdir = pwd;
repo = filesepStandard_startup(repo);
filename = [repo, '.gitmodules'];
if ~ispathvalid_startup(filename)
return;
end
cd(repo);
fid = fopen(filename, 'rt');
str... |
7995463bd922954b0d8f6df9313eec6cf8c18b06fc0edc1a1e304f95cc686565 | MATLAB | 1,096 | 37 | function axh = PlotTS(TSA, varargin)
opt_varargin = varargin;
defined_options = dictArray({ { 'MarkerSize', {5, {'numeric'}}},
{ 'Marker', {'k.', {'char'} } },
{ 'Offset', {0, {'numeric'} } },
... |
3f4afa5c1ab3ad54ef6cf474cd17a2c5152fe8f2f72d757ccef52f29c30f5b39 | MATLAB | 1,097 | 39 | function [t] = iscategorical(mat)
% Returns true if the matrix is a categorical regressors matrix.
%
% [T] = ISCATEGORICAL(MAT)
%
% This function will eventually replace CHECK_1OFN_REGRESSORS in
% in a future MVPA release.
% License:
%=====================================================================
%
% This is p... |
b1edaf1bebb53eb822c2b81d17351d29a8d481a19a5b4a116eefbbe9abc17de8 | MATLAB | 1,098 | 36 | function [perfmet] = perfmet_template(acts,targs,scratchpad,args)
% This is the template perfmet function for creating your own
%
% [PERFMET] = PERFMET_TEMPLATE(ACTS,TARGS,SCRATCHPAD,ARGS)
% License:
%=====================================================================
%
% This is part of the Princeton MVPA toolbox,... |
c902f68d9cfcd5db976bfc8bda81c401719b4bbef2ffe6717efd262dbdcca34b | MATLAB | 1,098 | 51 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% use linear regression to fit the 'slope', i.e. noise scaling needed to
% get the coh0 and coh aligned
function [a,r,m,n] = fitslope(x,y)
xorig = x;
x = abs(x);
y = abs(y);
%[t1, t2] = percthreshold(x, 0.5, 1, 0);
%t1 = prctile(x, 95);
if... |
2d5a8e5124c106e5eecce35bc7de0a8bc835c8882b4b5f743e682838606c72fc | MATLAB | 1,099 | 22 | %Fetches unique subject IDs for various experiments.
function [subjectIDs,sessions]=fetch_flicker_subjectIDs(root_dir,task_name)
metadata_tbl=readtable([root_dir '/FlickerStudyMetadata.xlsx'],'Sheet','Sessions','PreserveVariableNames',1);
metadata_tbl=metadata_tbl(:,{'Subject_ID','Experiment','Session','Sessio... |
98c7c523063616c112648796d999097bd090fcdec42ed495bbed260abf8776b1 | MATLAB | 1,100 | 28 | function h_MLE_pars = compute_hMLEpars_forsim(h_vals, prob_s_fun, J_i, eta_val, eps_val, n_obs)
% simulates the system H = eta_val*J_i*h*s_i + eps_val*s_i, drawing n_obs
% samples for the "true" h values provided in h_vals. From samples,
% computes the MLE parameters (estimate and SE of estimate).
% prob_s_fun is (1 +... |
91f14e2bfd3d4a6ff649e9f2f774b77fbe498646ab73a6e7d3c6082e2e6bc630 | MATLAB | 1,101 | 51 | function S = timeDeriv(tsa, varargin)
% TimeDerivative of a tsd
%
% USAGE:
% S = timeDeriv(tsa, OptionName, OptionValue, ...)
%
% This is intended for continuously sampled tsd-s,
% If there are some missing values, they are interpolated before smoothing
%
% INPUTS:
% tsa - a tsd object
%
% ... |
4ebbeeb44755e7dd79f4471e61c53bcc3d49e3dbb65de7ec257bd26c78de4fa2 | MATLAB | 1,102 | 26 | function [ t1, t2, t3 ] = PointsMaxCurvature_4CoE( Coefficients )
%% PointsMaxCurvature Find the frames of maximum curvature for a trace fit
%with a sigmoid curve (see createFit_sigmoid20210816) as described in
%Fedchyshyn and Wang, 2007. JPhysiology 581.2(581-602)
% Set the fourth derivative of the sigmoid equat... |
c695f36152ddada0bc9bad481c7047fc3d71a96630d23e108b533fa72787cc2a | MATLAB | 1,102 | 21 | function decoding_out = lda_test(labels_test,data_test,cfg,model)
if isstruct(data_test), error('This method requires training vectors in data_train directly. Probably a kernel was passed method is use. This method does not support kernel methods'), end
switch lower(cfg.decoding.method)
case 'classificatio... |
08b4f32d2ab1fa57442f4da92deb26437383533427fbb3408eae52adac3a1321 | MATLAB | 1,103 | 44 | function s = minus(a,b)
% Overload of the - operator
%
% USAGE:
% s = minus(a,b)
% %
% the - operator is defined to return a tsd with same timestamps and
% data that are the difference of the data. Returns error if timestamps of the
% two object don't coincide. One of the two operands may be a scalar
... |
321c8857eaabe4417f25b71f7e1ba298075704b6fda1da54d73698d1a2525d78 | MATLAB | 1,103 | 26 | function [ave_sizes, se_sizes, dur_bins, num_obs] = calculateAveSizeByDuration(sizes, durations)
% Calculates the average avalanche size by duration of avalanche. Allows
% creating duration bins larger than 1 (default dur_bin_size is 1). The
% min_obs_cutoff drops all duration bins with fewer than the specified
% numbe... |
6fe93a15da47406cd3abcc9b81892299dd3e048d752f6555c59d25c7a06683e7 | MATLAB | 1,103 | 60 | function B = subsref(A, S)
% overload of operator {} for element referencing. if subscripts are
% numieric, the correspondign elements of the array are returned, if
% subscript is a string, all the tsd's are returned that contain that
% string in their name
% copyright (c) 2004 Francesco P. Battaglia
% This softwar... |
c63d6af62b14f424663f07377c7d6011db156d2b19beffeb43e27afafe151996 | MATLAB | 1,104 | 42 |
ndip = 20;
snr = [0.6 0.5];
snr2 = 0.8;
amp = [0.7 0.8];%[0 0.2 0.3 0.4 0.5 0.6];%[0.2 0.4 0.6];
phs = 2.*pi.*[1/17 2/17 4/17 8/17];
patchsigma = 0;
N = 200;
state = rng;
%state = output.state;
for i0 = 1:100
for i1 = 1:numel(ndip)
for i2 = 1:numel(snr)
for i3 = 1:numel(snr2)
for i4 = 1:numel(amp)
... |
288d0c85ee347ff30d89a960fd994b14ecf3bbc301d3e10e4c0f621532ff514d | MATLAB | 1,105 | 57 | function [amp, phase, offset, rsquare, residuals, stdresid, trace] =...
fitsine(time, data, freq, const,ploton)
% [amp, phase (deg), rsquare, residuals, stdresid] = fitsine(time/dt, data, freq, const, ploton)
%% Parameters
if ~exist('const','var') || isempty(const)
const = 1;
end
if ~exist('ploton','var')
... |
2e36af5996baee4e18a00381f467592a153e408c6ee3c8f01ce618b21776d598 | MATLAB | 1,105 | 58 | function tsv = SnirfFile2Tsv(src, dst, options)
tsv = {};
% Parse args
if nargin==0
return
end
if ~isa(src, 'SnirfClass')
s = SnirfClass(src);
else
s = src;
end
if s.IsEmpty()
s.LoadStim(s.GetFilename());
end
if ~exist('dst','var')
dst = '';
end
if isempty(dst)
dst = s.GetStimTsvFilename();
en... |
5c7c4df05f7d9e76bf451bfac956bde33e9f712dda2ef40edeca4887bbe6f37a | MATLAB | 1,105 | 46 | function [syncZ,cchZ,cchP,cch,bxc] = SyncScore(t1,t2,bins)
% Computes a sync score for two spike trains (i.e. the number of z-values
% above the cross-correlogram when all fine temporal coordination
% is removed.
%
% USAGE:
% syncZ = SyncScore(t1,t2,bins,nbins)
%
% INPUTS
% t1 spike tr... |
dc4c4b5e37594a2af7bb74af5070052c750e0ed2c1529e441d05431bff639db5 | MATLAB | 1,105 | 26 | function events = left_trim_events(events, t, duration_sec)
fields = fieldnames(events);
nFields = size(fields,1);
for iField = 1:nFields
tmp=[];
cmd = sprintf('tmp = events.%s.on_ts;',fields{iField});eval(cmd);
i = find(tmp>duration_sec,1,'first');
cmd = sprintf('events.%s.o... |
7075b6c02a1927b59621dc9462751a9f386a2dc58d0f28cd23e4a24dee6b2dfc | MATLAB | 1,106 | 35 | blobDataNames={'Volume','Mean Intensity','Max Intensity','Convex Envelope','X',...
'Y','Elevation','Cell length','Cell width','Cell height',...
'OX Orientation','OY Orientation','OZ Orientation',...
'Cell fine elements','Length to width ratio','Distance traveled','Solidity','Ratio of volume to eq. diamet... |
169f8ab6936c9a749b5c4a4b080383b99e8d9afc294948bc1873ca3dedc2c561 | MATLAB | 1,110 | 57 | function a = gaussian_app(side, dims, sigma)
% A = GAUSSIAN_APP(SIDE, DIMS, SIGMA)
%
% Construct a Gaussian applicability.
%
% SIDE - Size of neighborhood along each dimension, should be odd.
% DIMS - Number of signal dimensions, must be between 1 and 4.
% SIGMA - Standard deviation of the Gaussian.
%
% Author:... |
c62619d8855f3382191af5295960b3abc7f5b8b3bc47c36fe848068677ae0583 | MATLAB | 1,112 | 35 | function [pmIM, alpha] = generateOverlayPhotobleachedLineOnOCT(json, y_um)
%Draw photobleach lines image to be overlayed ontop of OCT
%Onvert OCT image grid to original image
[xx_um,zz_um] = meshgrid(...
json.sectionIterationConfig.data_um.x.values, ...
json.sectionIterationConfig.data_um.z.values);
pmI... |
4a188ac80d0c2c4f50ac1ecbcd08645062879344a4a2fe3b0715c8ac576064ab | MATLAB | 1,113 | 55 | function [S,shank] = LoadMUAData(fbasename,varargin)
% Loads MUA data (cluster 1)
%
% USAGE:
% [S,shank] = LoadMUAData(fbasename)
%
% INPUTS:
% fbasename: file base name
%
% OUTPUTS:
% S: tsdArray of MUA (one cell element per electrode group)
% groups: electrode groups associated with each element
%
% OPTION:
% [S,s... |
4ea1235e3bc31b8101e0db00109c21fb23986bfee9dbe1ec1ff5a57926d16d9d | MATLAB | 1,113 | 40 | %function [State, hmm, decode] = gausshmm(Fet, nStates, updateOM, verbose)
% train HMM software using a Gaussian observation
% model of Fet. nStates - number of mixtures/states
% updateOM - if to update the observation model
function [State, hmm, decode] = gausshmm(Fet, varargin)
[nStates, updateOM, verbose] = Default... |
68a9db69655b10d7064eaa53245e62a98583139e37a0b827c6a9dfb58c79a346 | MATLAB | 1,113 | 68 | function O = union(varargin)
% Computes the union of intervalSet's
%
% USAGE:
% O = union(O1, O2, ..., On)
%
% INPUTS:
% O1, O2, ..., On - intervalSet objects
%
% OUTPUTS:
% O - union intervalSet object
% copyright (c) 2004 Francesco P. Battaglia, debugging by Adrien Peyrache 2007
% This softwar... |
a77f072188024fd5653ca5ca5c2ecbd61bdee3e6a25eff80ecd5e0a96ac83cde | MATLAB | 1,113 | 46 |
% videoPath = 'E:\NAS_SD\SuiviClient\Triffilieff\AnnaRoman\DataAnna_Baseline\M27322\M27322_20210709_sess4_rec3_SWE.avi';
videoPath = 'E:\NAS_SD\SuiviClient\Triffilieff\AnnaRoman\DataAnna_Baseline\Msp446\Msp446_20210721_sess9_rec2_SWE.avi';
v = VideoReader(videoPath);
nFrames = 100;
beginningOffset_sec = 120;
interFr... |
d14b7950c6eb7d9a7f4fe4c9a2f40df662574caaab841f9e55d0180915ee9e71 | MATLAB | 1,113 | 36 | %% Frechet Distance calculation
% Run AFTER full Block and Experiment code was run
% Written by Alice Mosberger and Leslie Sibener
% Version Jan 2021
% Groups are treated separately
load(DataPath);
%% First reorganize the data and clear unnecessary variables
for g = 1:NumGroups
for a = 1:Main(g).Num... |
0f1ad2b47f6cb1b0387bc3d23db915ad4d4d6a3aef88ab3e41a9f8088be6c2b2 | MATLAB | 1,114 | 39 | function [isthere] = exist_objsubfield(subj,objtype,objname,fieldname,subfieldname)
% Checks whether the subfield exists
%
% [ISTHERE] = EXIST_SUBFIELD(SUBJ,OBJTYPE,OBJNAME,FIELDNAME,SUBFIELDNAME)
%
% Checks whether the SUBFIELDNAME exists inside the FIELD of the
% object OBJNAME of OBJTYPE.
%
% Returns true if it doe... |
14af37524511f474e7459054b02ebc5457a6f1273f9056cf2174b264ba324e63 | MATLAB | 1,114 | 44 | function plotmat(matrix, textcolour, gridcolour, fontsize)
%PLOTMAT Display a matrix.
%
% Description
% PLOTMAT(MATRIX, TEXTCOLOUR, GRIDCOLOUR, FONTSIZE) displays the matrix
% MATRIX on the current figure. The TEXTCOLOUR and GRIDCOLOUR
% arguments control the colours of the numbers and grid labels
% respectively and s... |
2e5935050724d078d84313e883de82f35edec415aa1d19f68f4b31c98544f929 | MATLAB | 1,114 | 31 | function [clabel,dval,prob] = test_lda(cf,X)
% Applies an LDA classifier to test data and produces class labels,
% decision values, and posterior probabilities.
%
% Usage:
% [clabel,dval] = test_lda(cf,X)
%
%Parameters:
% cf - struct describing the classifier obtained from training
% dat... |
1ff6aac43cd7992c3f12b6d11a2067bd4e291ec3ff517efec0486bc2ba4d8c5d | MATLAB | 1,115 | 29 | % reshape index from (chn x cond x conc) to just chn
% mlList is list of all (chn x cond x cond) and can be found in dcAvg.measurementList
% given list of chn index, find all conditions and conc belonging to chn
% list.
% mlList increase conc first, next increase chn, next increase cond
function [reshapeIdx] = reshape... |
ed84477aaef4340dadc07efabfeae0c2c2e5132a803c8734399601434662036c | MATLAB | 1,115 | 42 | function DistributionWholeImage(exportFolder, fileExportFolder, fileParams, flowDistParams)
%% Import Parameters
% File Parameters
thetaInDegrees = fileParams.thetaInDegrees;
thetaInRadians = fileParams.thetaInRadians;
% Figure Parameters
dataBinWidth = flowDistParams.dataBinWidth;
%% Load Files
% Main Analysis Ima... |
05cc23dd357440910698615c172e51e2d28703e7bb102f623bf19a047f9b330c | MATLAB | 1,116 | 43 | function net = rbfunpak(net, w)
%RBFUNPAK Separates a vector of RBF weights into its components.
%
% Description
% NET = RBFUNPAK(NET, W) takes an RBF network data structure NET and a
% weight vector W, and returns a network data structure identical to
% the input network, except that the centres C, the widths WI, the... |
91f23a15241a42533195528727ab7f6f0226fe69b6c6babe4e91b733f32d664c | MATLAB | 1,116 | 34 | function ciplot(lower,upper,x,colour)
% ciplot(lower,upper)
% ciplot(lower,upper,x)
% ciplot(lower,upper,x,colour)
%
% Plots a shaded region on a graph between specified lower and upper confidence intervals (L and U).
% l and u must be vectors of the same length.
% Uses the 'fill' function, not 'ar... |
b4152559580d9314543cfebe5e4b67b6a1f410ca09a591afa2d30fc43ff78307 | MATLAB | 1,116 | 60 | %% This script generates panels of figures from source data
% Please make sure the folder "Data" from the source data is extracted
% directly at the root directory of the github code, so that it contains:
% github_dir\Data\
% github_dir\Data\Neuro\
% github_dir\Data\Behavior\
% etc.
% and from the code repository:
%... |
b041ec69004eea895e904678b0ed2ceb37edc579480dba2c66c00e49daa997f0 | MATLAB | 1,118 | 32 | function [subj new_regsname] = binarize_regressors(subj,old_regsname,thresh,varargin)
% [SUBJ NEW_REGSNAME] = BINARIZE_REGRESSORS(SUBJ,OLD_REGSNAME,THRESH, ...)
%
% Takes in a regressors object, and sets all values below THRESH to 0,
% and all values above THRESH to 1.
%
% Gets called by CONVOLVE_REGRESSORS_AFNI.
%
% ... |
43ac2453dfff89db4677b5688f4b88a41ac1e32c1d5619c8b886d33ce3fc23f6 | MATLAB | 1,119 | 41 | function [xf] = generate_target_wave( image_size, dt, T, frequency, lambda, varargin )
% *WAVE*
%
% GENERATE TARGET WAVE TEST DATA generates a simple test dataset for
% use with the functions in WAVE
%
% data description: a 2d target wave
%
% INPUT
% image si... |
6de64f4b5e163cc71c8188dd28b5bb414e8745190ebd5186cf8a19a6064601f5 | MATLAB | 1,119 | 47 | function [st, clu, neuronPos] = mhpSim(N, muMaxN, numSpikes, maxEig, conType, varargin)
if conType == "random"
if nargin == 6
Y = double(rand(N, N) < varargin{1});
Y = Y*maxEig/max(abs(eig(Y)));
neuronPos = [];
else
disp("Error: invalid input.");
return;
end
... |
6e00ede3273de0c069eabe4c464b8c043795ab10346fbaddc6bebde7ea4dfc7f | MATLAB | 1,121 | 36 | function net = glminit(net, prior)
%GLMINIT Initialise the weights in a generalized linear model.
%
% Description
%
% NET = GLMINIT(NET, PRIOR) takes a generalized linear model NET and
% sets the weights and biases by sampling from a Gaussian distribution.
% If PRIOR is a scalar, then all of the parameters (weights and... |
30801c074ecaa1ded3f6d1e40e960ffb3e3a16709b2b27a4cfec7037edd1ee85 | MATLAB | 1,123 | 33 | function [mappedX, W, mu_X] = prewhiten(X)
%PREWHITEN Performs prewhitening of a dataset X
%
% [X, W, mu_X] = prewhiten(X)
%
% Performs prewhitening of the dataset X. Prewhitening concentrates the main
% variance in the data in a relatively small number of dimensions, and
% removes all first-order structure from the... |
9d486c2f9302a1fe71300b848a55cf016bc0dde2547ebb34fe74ecaad0676fb4 | MATLAB | 1,123 | 58 | function [pval, chisq_dat, chisq_rnd, Or_list] = randomization_test(Oi, Ei, niter)
%tic
if ~exist('niter', 'var')
niter = 1e4;
end
%Oi(Oi == 0) = 0.5;
Ei(Ei == 0) = 0.5;
Oi = round(Oi);
% from Ei get pi, which is the model Oi is being compared against
ntr = repmat(sum(Ei, 2)', size(Ei, 2),1)';
pi = Ei./ntr;
nO... |
e4b227b95cad9d6b234a050a069c2c498e506502a131a2b478399d5b7f6fdbaa | MATLAB | 1,124 | 43 | %% Plot V4 MI Firing Rate d' and bias split at cued and cue-opposite locations (histogram)
%% Code
loc = ["cued","opp"];
loc_flag = 1;% input('neural data at cued location or cue-opposite location: 1-cued, 2-opp: '); % loc_flag = 1 for Fig 2D, loc_flag = 2 for Fig 3B
% cue epoch
win_start = 500;
win_end = 2500;
win_s... |
b0151d7e8af838638f9210e19b37387ade6cfff91e73475ecf749d7846568d95 | MATLAB | 1,125 | 29 | function histologyToOCTT = knobesToTransform( ...
scale_percent,rotation_deg,xTranslation_um,zTranslation_um, histologyScale_umperpix, octScale_umperpix)
% For explanation about the tranformation see website:
% scale_percent - negative is shrinkage
% histologyScale_umperpix - size of histology image scanned,
... |
b82f75c1a0bacb73e9b21a37a667f41ad4f2a9ef1cb156bf64eb08ec1cb450a1 | MATLAB | 1,125 | 44 | function covf = gpcovarf(net, x1, x2)
%GPCOVARF Calculate the covariance function for a Gaussian Process.
%
% Description
%
% COVF = GPCOVARF(NET, X1, X2) takes a Gaussian Process data structure
% NET together with two matrices X1 and X2 of input vectors, and
% computes the matrix of the covariance function values CO... |
fb566c7cf75898a69de5c4132b24cd7610671a9ef5bab6886adac0f40decf043 | MATLAB | 1,125 | 37 | function [tv,g]=tvar(x,percent)
% function [tv]=tvar(x,percent)
% Returns the estimated squared standard error of the trimmed mean of x.
% x must be a vector. If x is empty, then NaN is returned.
% percent must be a number between 0 and 100
%
% The trimmed variance is calculated from the winsorized variance, vw,
% acc... |
d87ee163f1fdcda69dc9fe31a86f4cc2ffa3b418fa10f4b59d69e07542947a21 | MATLAB | 1,127 | 39 | function net = mlpunpak(net, w)
%MLPUNPAK Separates weights vector into weight and bias matrices.
%
% Description
% NET = MLPUNPAK(NET, W) takes an mlp network data structure NET and a
% weight vector W, and returns a network data structure identical to
% the input network, except that the first-layer weight matrix W... |
018a8feed7a8de1a3f1b00224f930d733c6462d9a14951b7665ba0a692b75e83 | MATLAB | 1,128 | 24 | function step1 = analysis_step1(f, step1)
%% LOAD DORIC DATA
[step1.raw_signals, step1.dein_signals] = doric_tools.open_doric(f, step1);
plot_tools.photo_plots(step1, 'deinterleaved signals');
%% LEFT TRIM TO REMOVE STRONG PHOTOBLEATCHING AT THE BEGINNING
step1.left_trim_dur_sec = 15;
[step1.dein_signals.time, step1.... |
24119cacf015934a15805a7213e7f2895e275721c3c803c0b7bda617ceda897e | MATLAB | 1,130 | 39 | % Preprocessing unit test
%
% demean
tol = 10e-10;
% Random data
X = randn(145,40,20,3) - 10;
% Get default parameters
param = mv_get_preprocess_param('demean');
%% demean along dimension X should result in all mean = 0
for dd=1:ndims(X)
param.dimension = dd;
[~, Xd] = mv_preprocess_demean(param, X);
m ... |
b5705dffbc4b5f3d6126f625420d9a5f25e4f5f4b19a55c51279da771cde5a25 | MATLAB | 1,130 | 36 | function [regs] = fake_smooth_regs(nConds, nTimepoints, noisiness)
% [REGS] = FAKE_SMOOTH_REGS(NCONDS, NTIMEPOINTS, NOISINESS)
%
% Randomly generates nConds' worth of sine waves at roughly
% the same frequency, shifted relative to one another.
%
% e.g. regs = fake_smooth_regs(3, 240, 0.1);
% choose a random frequenc... |
dd6bf072c3a58eec3bd4529203af28572237f53e5062d51c30c1d222e8f41f6c | MATLAB | 1,130 | 66 | function [err,p,f] = GetPath (s, allmc)
%
% [err,PathString,FileString] = GetPath (s, allmc)
%
%Purpose:
% Breaks the string s into a path and file part
%
%
%Input Parameters:
% s is a string like How/Didley/Doo
% allmc : 1 --> search for path using both types of file-separators / and \
% 0 --> ... |
f8769d7d56f9f9b8f3e732253e00ca7469791115c5181fa8cc599bedfb2eded7 | MATLAB | 1,130 | 44 | %
% calculates the coefficient of variation metric CV2, as described in Holt et al 1996, J Neurophysiol
%
% ISIs are in sec and expected to be in order
%
%
%returns:
%CV2: mean CV2 over all ranges
%CV2_all: CV2 for each pair of consecutive ISIs
%CV2_all_diff: the difference between each consecutive ISIs, useful to calc... |
84e5ec45ce900b70aab2733c0b09132f3fb23c6808063352f1048d59e0d9b1ab | MATLAB | 1,133 | 61 | function ac = compressLogicalArray(a)
ac = [];
if isempty(a)
return;
end
if all(a==1)
ac = [1,length(a), 1];
return
end
if all(a==0)
ac = [1,length(a), 0];
return
end
k = find(a==0);
kk = 1;
% Generate all zero intervals
for ii = 1:length(k)
if ii == 1
iS = k(ii);
iE = k(ii);
... |
3af387ba8937cec37bed339411a32019a734f1a35cf51b897ff59b3711d2240b | MATLAB | 1,134 | 40 | 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 matri... |
4b8896584474034958e44814453b396354465b9b114a0ecb5fab425eb03b608d | MATLAB | 1,134 | 34 | function test_suite = test_bids_query_nirs %#ok<*STOUT>
try % assignment of 'localfunctions' is necessary in Matlab >= 2016
test_functions = localfunctions(); %#ok<*NASGU>
catch % no problem; early Matlab versions can use initTestSuite fine
end
initTestSuite;
end
function test_bids_query_emg_basic()
%
... |
465b9016562dac7f8401161fc890a5c6c08541523a48ec7165b935927ea6e0c5 | MATLAB | 1,135 | 42 | function DistributionWholeImageOverTime(exportFolder, fileExportFolder, fileParams, flowDistParams)
%% Import Parameters
% File Parameters
thetaInDegrees = fileParams.thetaInDegrees;
thetaInRadians = fileParams.thetaInRadians;
% Figure Parameters
dataBinWidth = flowDistParams.dataBinWidth;
%% Load Files
% Main Anal... |
5c2a4849eded2fbd0916e1a824fb55ffcaa9a169f643688de75efdcf75f41e20 | MATLAB | 1,135 | 39 | function [ssmp] = nansum(x, dim)
% [S] = NANSUM(X, DIM) computes the sum, across all cells in x along
% the dimension dim, accounting for NaNs.
%
% X should be an linear cell-array of matrices for which the size in at
% least one of the dimensions should be the same for all cells
D = checkinput(x);
if nargin==1 |... |
b6c09b3bf816b591f8d0af87c99831b71e20c9159104bf28f1aa23b9347e031b | MATLAB | 1,135 | 54 | function O = regularIntervals(start, stop, i_length, step, varargin);
% O = regularIntervals(start, stop, length, step) returns an intervalSet
% with intervals of constant length
%
% INPUTS:
% start, stop: of the period spanned by the intervalSet (intervalSet
% guaranteed to cover the period)
% length: length of each... |
df13727aae682bf7768a98df77853e4b377183e36264dd059123f23c1ed640a1 | MATLAB | 1,135 | 37 | % zeke barger
% 070419
% create a multi-taper spectrogram of EEG data
% s is the spectrogram, t is the time axis, f is the frequency axis
function [s, t, f] = createSpectrogram(EEG, SR, winstep)
window = max([5, winstep]);
params = struct;
params.pad = -1;
params.Fs = SR;
params.fpass = [0 64];
params.tap... |
64efcfd354684ec05e0371c32aadd74af1a4d22ac7fd0ce42e8753ee625c24f9 | MATLAB | 1,136 | 36 | function [hh,fg,cb] = plot_vector_field( ph, varargin )
% *WAVE*
%
% PLOT VECTOR FIELD
%
% INPUT
% ph - complex-valued scalar field representing vector directions
%
% OUTPUT
% vector field plot
%
% checks
assert( ~isreal(ph), 'complex-valued input required, ph' )
% set defaults
if nargin > 1, plot_option = varargin{1... |
f4c024c8aff618c316bb5e8a97941ce18bcc64cfc0c35f53735a77aafe262535 | MATLAB | 1,137 | 55 | function R = regIntervals(ep,N)
% Split an intervalSet object in N segments of equal length
%
% USAGE
% R = regIntervals(ep,N)
%
% INPUTS:
% ep: original intervalSet
% N: number of desired segments
%
% OUTPUT:
% R: a cell array of splitted intervalSet objects
% copyright (c) 2004-2011 Francesc... |
a144295d907c06a86c60f7efed454f9c18a43cb534949f6dbd51611bfd1636f0 | MATLAB | 1,138 | 29 | function [datasetPath, datasetName] = s3GetPathToLatestDataset (imageResolution,datasetTag)
% imageResolution can be '2x','4x','10x' etc
% datasetTag can be additional search phrase, or can be empty (default)
%% Inputs
if ~exist('datasetTag','var')
datasetTag = '';
end
datasetTag = strtrim(datasetTag);
... |
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