sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cb8a3013029e0d55d5be73ebb311f41e5ab74189642ee403b6bf3e61a40f2340 | MATLAB | 1,479 | 70 | function LAN = erplab2lan(file,setfile)
% <°LAN)<] toolbox
% v.0.1
% load .erp file (ERPLAB) with the corresponding .set file (EEGLAB)
% file = name (and path) of .erp file [ 'file.erp' ]
% setfile = name (and path) of .set file [ 'file.set' ]
%
% Pablo Billeke
% 29.08.2013
load(file,'-mat');
if nargin==1
... |
33f1667e894448d9a91357806420379509b40a5fcd0ebf1cdcc6144e0dbc864c | MATLAB | 1,480 | 60 | %% var2trfun
%
% Calculate VAR transfer function from VAR coefficients
%
% <matlab:open('var2trfun.m') code>
%
%% Syntax
%
% H = var2trfun(A,fres)
%
%% Arguments
%
% See also <mvgchelp.html#4 Common variable names and data structures>.
%
% _input_
%
% A VAR coefficients matrix
% fres frequenc... |
42a6aac9a04ae47de4a3abba66deb0312666095477e060fe7e6c6e405c01f239 | MATLAB | 1,480 | 35 | % FMM3D: MATLAB/Octave wrappers to 3D fast multipole methods.
% Center for Computational Mathematics, Flatiron Institute.
%
% Functions:
% lfmm3d - FMM in 3D for Laplace (electrostatic) kernels.
% l3ddir - Direct (slow) 3D Laplace kernel sums (reference for LFMM3D).
% hfmm3d - FMM in 3D for Helmholtz... |
70a9a1862699e40094b107d5a8e798d640970a8cd5dae9c47eb23bec9b628492 | MATLAB | 1,480 | 1 | % TSSET Set a field in the Experiment structure
% TSSETTRIAL(TRIALNAME) sets TRIALNAME as the active trial that will be
% used for computing statistics.
%
% When a trial is defined, it becomes the active trial.
%
% See also TSsetdata, TSsetoverwritemode, TStrialstat
%%% FIX ABOVE
function TSset(arg1,arg2,arg... |
f31f361b9d449a20d56ca428c0cc0e312b5e045ded5404d4cec30c7bdd26aaf5 | MATLAB | 1,480 | 37 | function y_ChangeImgPrefix(InputDir,CurrentPrefix,WantedPrefix)
% y_ChangeImgPrefix(InputDir,CurrentPrefix,WantedPrefix)
% Change the prefix of images in the sub-directories.
% InputDir - where the data stores
% CurrentPrefix - the current prefix of the images.
% WantedPrefix - The wanted prefix.
% Exampl... |
f71e68f0533ebd4f34ebec2a6ab6f823b524bcb980a944fdc542065d23211021 | MATLAB | 1,480 | 56 | function lan_master_gui_spks_clu(spikes, clu)
figure
choice = 1;
dimx = 1;
dimy = 2;
ccfg = struct('feature', 'wav', 'scales', 4, 'inputs', 10);
inspk = wave_features(spikes, ccfg);
uicontrol('style', 'text', 'string', 'dim x',...
'units', 'norm', 'position', [.1 .0 .1 .07]);
uicontrol('style', 'edit', 'string'... |
77d48bde6bf15f77801fe6e757156394cc8fa17c976dfb827d28b1e947f3eeb9 | MATLAB | 1,481 | 50 | %% 4-PANEL TEXTURE DEMO (will take <1min per iteration)
%
% This version of the model computes parameters within nine windows that
% tile the image. It is NOT the same as the model used in the paper,
% but runs substantially faster, so is a good way to make sure
% that the code is working. The resulting synthetic imag... |
0ee68528352fbfa3e7e097790413066f76c8470369ef28689dc83db5669be80b | MATLAB | 1,482 | 60 | function c = SubjectColors(subjectID, cb)
if nargin == 1
cb = false; % Colorblind alternatives
end
% Get multiple from ordered cell array
if length(subjectID) > 1 && isa(subjectID , 'cell')
c = zeros(length(subjectID),3);
for i = 1:length(subjectID)
c(i,:) = Sub... |
11cd57f90042555604b83508a8fc1e93c14be2f597ff33cacbb36b9f2d682839 | MATLAB | 1,482 | 50 | function [pZ, pX] = noisyMixModelInferNodes(model, Y, softev)
% Y is Ndims * Nnodes
% so Y(:,j) are the observations for node j
%
% Model is Z -> Xj -> Yj
%
% pZ(k) responsibility of cluster k
% pX(c, j) = p(Xj = c)
Nmix = model.mixmodel.nmix;
Nstates = model.Nstates;
Nnodes = model.Nnodes;
logMix = log(rowve... |
fbe7ea440ccb165532a88dadd0ce088236a649427aac86f88899f709344c4dab | MATLAB | 1,482 | 54 | % changeaxisunits(factorx,factory)
% changeaxisunits(factorx,factory,hax)
% Changes the units of the x and y axes.
% Suppose the original units of the x axis is frames and the original unit
% of the y-axis is pixels, and we want to change to seconds and
% centimeters, respectively. If a frame is .05 seconds and a pixe... |
7cb385d8c16dee7ea8cea9ed92fa8d95c27d047e74a6e5cfb122e59f0f21d489 | MATLAB | 1,483 | 74 | function LAN = cnt2lan(cfg)
% v.0.2
% Pablo Billeke
% from EEGLAB
%
% 12.04.2016 improve RT extraction
if nargin == 0
[filename, filepath] = uigetfile('*.CNT;*.cnt', 'Choose a CNT file -- cnt2lan()');
else
if isstruct(cfg)
filename = getcfg(cfg,'filename');
filepath = getcfg(cfg,'filepath','... |
f2cae1fda014c4b113ebe074b1e5a2e9f14f74f96959e448cfb564e58fffe58b | MATLAB | 1,483 | 57 | function [FitCC,CC,coef]=FitTemporalPattern(Data,Labels,NumTests)
% How well is the neural response to an "action" that combines two
% movements explained by the neural response to those movements alone?
%%
X1=Data{1};
X2=Data{2};
Y=Data{3};
if nargin<2 || isempty(Labels); Labels=1:size(X1,2); end
if nargin<3; NumTes... |
413b5757efff92785ea0ae020d72deb4f9356826b1f02f9ff479314cddae411b | MATLAB | 1,484 | 68 | %% Find the mode of a mixture of 2, 1D Gaussians using Simulated Annealing
%
%%
% This file is from pmtk3.googlecode.com
function saDemoMOG()
sigma_prop = 10; % Standard deviation of the Gaussian proposal.
seed = 1; randn('state', seed); rand('state', seed);
xinit = 20*rand(1,1); % initial state
Ns... |
fa764269c8b8b9479f051bc2ba5d5b5e05084bf2a8d3b42b9771d3beb016dc9f | MATLAB | 1,484 | 52 | function [CC]=ComputeTemporalConsistency(Data,Labels,NumTests)
% Test to see if one condition (column) is reliably the larger then all
% other columns across random 50/5-0 NumTests in the data
% Data : Number of samples X number of conditions.
% labels Optional condition names
% NumTests Number of NumTests
%
% Reli... |
a75ad629c97aea8abfee7c2da3779444d24caeac4d9cceeee3c0b7e330ff441a | MATLAB | 1,485 | 26 | disp('############################################');
disp('#### Design a cone trajectory ####');
disp('#### ####');
disp('############################################');
disp(' ');
r = linspace(0,5, 500)';
th = linspace(0,2*pi, 500)';
C = r.*exp(2*pi*1i*th);
C = [real(C) i... |
69b4fd0638fe1e3b01d384ab63ee52e81ac0d49a486c0aeb96393d212e5eeeb7 | MATLAB | 1,486 | 56 | function [binnedx, binnedy, binnedz, stdx, stdy, stdz] = divideintobins3(x, y, z, nbins)
% take two vectors and divide x them into nbins, then compute the mean
% response of y for each x
if ~exist('corrtype', 'var'); corrtype = 'Spearman'; end
%assert(~any(isnan(x)), 'x contains nans');
%assert(~any(isnan(y)), 'y cont... |
7227bbb39ef90e5e3aabd714ab015ea78a75d755b2b4561bcdbd06a72f0c1df3 | MATLAB | 1,486 | 31 | function plot_sectors_2(this_center, circle_rad, sector_endpoints, random_color_red_colony, theta)
num_sectors = length(sector_endpoints)/2;
sector_points = zeros(length(theta) + 2,2);
sector_points(1,:) = this_center;
sector_points(end,:) = this_center;
% If the colony should be cured
if num_sectors == 1/2
%se... |
b0f5ba5d5200c771a47b8a634f68bd3c809f3671835f02ac1be10b5bf173d12d | MATLAB | 1,486 | 51 | clear all; close all;
% SYNTAX
% example_global_smoothing_lumped_laplace
% DESCRIPTION
% This script performs global (or local) iterative Laplacian mesh
% smoothing using the lumped-smoothing algorithm. The smoothing improves
% triangle quality and increases min edge length but deforms the mesh
%
% Low-... |
ffc54f01c8ab365aafcd8923acfdf9e39a41e870da7834a87f09768f70aef1a9 | MATLAB | 1,486 | 47 | function a = extract(t,srchsubs)
%EXTRACT Extract value for a sptensor.
%
% EXTRACT(X,SUBS) returns a list of values.
%
% See also SPTENSOR/SUBSREF.
%
%MATLAB Tensor Toolbox.
%Copyright 2015, Sandia Corporation.
% This is the MATLAB Tensor Toolbox by T. Kolda, B. Bader, and others.
% http://www.sandia.gov/~tgkold... |
219389f16a36f4cd75bc72f905cade97cff225db4bfd0d222347c46d3e245832 | MATLAB | 1,487 | 55 | function Is = anisdiff(I,sigI,NIter);
if nargin < 3,
NIter = 4;
if nargin < 2,
sigI = 10;
end;
end;
% Function that diffuse an image anisotropially.
Is = I;
[ny,nx] = size(I);
c_n = zeros(ny-2,nx-2);
c_s = zeros(ny-2,nx-2);
c_w = zeros(ny-2,nx-2);
c_e = zeros(ny-2,nx-2);
c_nw = zeros(ny-2,nx-2);
c_ne = ze... |
876eebd087d20fadf85bf97d28a6c84c2d61c5d056f83669e14dfc03fe6d7fb3 | MATLAB | 1,487 | 53 | function R = randrot(n, N)
% Generates uniformly random rotation matrices.
%
% function R = randrot(n, N)
%
% R is a n-by-n-by-N matrix such that each slice R(:, :, i) is an
% orthogonal matrix of size n of determinant +1 (i.e., a matrix in SO(n)).
% By default, N = 1.
% Complexity: N times O(n^3).
% Theory in... |
95b25341f8e7774850a82328093accde8aa4344e085712938f796119a0df6a39 | MATLAB | 1,487 | 67 | function [Kp stdKp] = Patlak(tissue,time_tissue,Cp,Cpint,weights,nrpoints)
% NOTA IMPORTANTE
%Cp e Cpint devono essere interpolati sulla griglia dei tempi definita da
%time_tissue
% Cp = interp1(tnew,Cpnew,time);
% Cplint = cumtrapz(tnew,Cpnew);
% Cpint = interp1(tnew,Cplint,time);
% nrpoints = 10;
%Check s... |
b9b46ac9a46d1c835cd8d2e7bacd6f671322ebb9893654f377bc955cfaae247d | MATLAB | 1,487 | 38 | function [azi,ele]=hor2sph(lat,pol)
%HOR2SPH transform horizontal-polar to spherical coordinates.
% [azi,ele]=hor2sph(lat,pol)
%
% Input:
% lat ... lateral angle (-90 <= lat <= 90)
% pol ... polar angle (-90 <= pol < 270)
%
% Output:
% azi ... azimuth (0 <= azi < 360)
% ele ... elevatio... |
dde7b28fe9db029dd9890f9dc709f8745592646793199a7ced1e4f467e3ecb39 | MATLAB | 1,487 | 37 | function ret = make_links_in_registration()
ret = true;
loadParameters;
src_dir = relpath(params.registeredImagesDir,params.normalizedImagesDir);
old_dir = pwd;
cd(params.registeredImagesDir);
for c_i = 1:length(regparams.CHANNELS)
normalized_filename = fullfile(src_dir,sprintf('%s_r... |
fdcb5d2ae64ee20b71c551a11906f9ec5eb37776d4af40a465ba635694db7764 | MATLAB | 1,487 | 52 | function outpoints = y_tal2icbm_spm(inpoints)
%
% This function converts coordinates from Talairach space to MNI
% space (normalized using the SPM software package) using the
% tal2icbm transform developed and validated by Jack Lancaster
% at the Research Imaging Center in San Antonio, Texas.
%
% http://www3.intersci... |
6f9f3e30f97acc85b968255d63d6d5ddd42e7208575e5e31131c74fe5ad7d974 | MATLAB | 1,488 | 49 | function b = myregress(y,X,varargin)
%MYREGRESS Multiple linear regression using least squares.
% B = MYREGRESS(Y,X) returns the matrix B of regression coefficients in the
% linear model Y = X*B. X is an n-by-dx design matrix, with rows
% corresponding to observations and columns to predictor variables. Y is
% ... |
a94df201de70a58dcfe35165f73e74aa39c44f46e31ff07cff292be9aaeb7d43 | MATLAB | 1,488 | 64 | function logp = gaussInvWishartLogprob(arg1, arg2, arg3, arg4, arg5, arg6)
% logp(i) = p(m(:, i), S(:, :, i) | model)
% logp = gaussInvWishartLogprob(model, m, S) OR
% logp = gaussInvWishartLogprob(mu, Sigma, dof, k, m, S)
%
% logp(i) = p(m(:, i), S(:, :, i) | model)
% = N(m(:, i) | model.mu, (1/model.k) * S(... |
d30d9ed5fdfa312389b85540629484201c0e480ad39372953e4e11fd5b73f4ec | MATLAB | 1,488 | 40 | function datToNPY(inFilename, outFilename, dataType, shape, varargin)
% function datToNPY(inFilename, outFilename, shape, dataType, [fortranOrder, littleEndian])
%
% make a NPY file from a flat binary file, given that you know the shape,
% dataType, ordering, and endianness of the flat binary file.
%
% The point here... |
e5ef47b2dae1e29ea01e7add83bbbce6643c65025a2be7648e3c0112bb853c7b | MATLAB | 1,488 | 37 | function [pts] = generateHexSubunitGrid(NsubMax)
%GENERATEHEXSUBUNITGRID Generates a hexagonal grid of subunit locations.
%
% This function creates a hexagonal grid of points with unit spacing,
% centered at (0,0). The grid is designed to accommodate up to NsubMax
% subunits, ensuring that the points are arrang... |
badd92e3923057e548d90aa5d17d4b136acd8f66ea33024fd8bfa3f2162f64cf | MATLAB | 1,489 | 72 | function sdata = stack(data, options)
stack_id = 0;
fn = fieldnames(data);
sdata = struct;
for j = 1:length(fn)
sdata.(fn{j}) = [];
end
for i = 1:length(data)
if data(i).time_offset == 0
stack_id = stack_id + 1;
for j = 1:length(fn)
sdata(stack_id).(fn{j}) = [];
end
end
% add to the current ... |
267696f866886e6bc614f39a8bbdb69564081b2e6fa112f241d11c3ed60b57d5 | MATLAB | 1,490 | 45 | function [trl, event] = ft_trialfun_example1(cfg)
% FT_TRIALFUN_EXAMPLE1 is an example trial function. It searches for events
% of type "trigger" and specifically for a trigger with value 7, followed
% by a trigger with value 64.
%
% You would use this function as follows
% cfg = [];
% cfg.dataset ... |
0d0ccedeb768c2351c61dd7c3e59da83f44eab38791103630eb20d562fd37d47 | MATLAB | 1,491 | 38 |
data = dir('/DATAPOOL/ERRORMONITORING/SEM_mri_data/P*');
%%
sub = 1;
for i = 1:size(data,1)
data_anat = [data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/nifti/anat'];
anat_files = dir(fullfile(data_anat, "*.nii"));
def_field = anat_files(startsWith(string(char(anat_files.name)),... |
1c1404010f0aaeddc9d552970f354e535642b152b8bdcfa39e832c49c405bdc8 | MATLAB | 1,491 | 43 | function [keypoint reRun precomp_grads] = Create_Descriptor(pix, xyScale, tScale, x, y, z, sift_params, precomp_grads)
% Main function of 3DSIFT Program from http://www.cs.ucf.edu/~pscovann/
%
% Inputs:
% pix - a 3 dimensional matrix of uint8
% xyScale and tScale - affects both the scale and the resolution, these... |
2439809f4db8cbc2f763454d8afef709fa5eb60296a956bb3bbd84e0f686c559 | MATLAB | 1,491 | 66 | addpath(genpath('/groups/branson/home/bransonk/tracking/code/piotr_toolbox_V3.02'));
addpath /groups/branson/home/bransonk/behavioranalysis/code/Jdetect/Jdetect/misc;
addpath /groups/branson/home/bransonk/behavioranalysis/code/Jdetect/Jdetect/filehandling;
folder = '../headTracking';
file = 'FlyHeadStephenCuratedData_... |
4efa6b6a36db33df13625f53ec216382d60fa350b47ae74db3c35c077a1ea7a6 | MATLAB | 1,491 | 51 | %% ------------------------------ Initialize ------------------------------
% include all functions
addpath(genpath('src'));
parameters;
% summary variable
summary = {};
% TODO: Somos centro detekcija imant sankirtą su branduoliais
% TODO: Ląstelės branduolio detekcija: branduolys turintis didžiausią sankirtos tūrį ... |
1379008f607ccfb521d8665bb67129b1257a165131c0de90e47ba4c640fbaca4 | MATLAB | 1,492 | 55 | function [normal,normalf] = compute_normal(vertex,face)
% compute_normal - compute the normal of a triangulation
%
% [normal,normalf] = compute_normal(vertex,face);
%
% normal(i,:) is the normal at vertex i.
% normalf(j,:) is the normal at face j.
%
% Copyright (c) 2004 Gabriel Peyré
[vertex,face] ... |
38f66d951d92504d42d499aed31906857bb78187f61c05042cb1366eb17f2693 | MATLAB | 1,492 | 41 | function [gx,dgdx,dgdp] = g_2AFC_basis(x,P,u,in)
% 2AFC observation function: projection onto basis function set
% function [gx,dgdx,dgdp] = g_2AFC_basis(x,P,u,in)
% This function evaluates the probability of choosing the first alternative
% options in a 2 alternative forced choice paradigm, where each option is
% decr... |
43c5e5856edaf1d1624a3abb2876be8135091d2184ef98755f67328360e5ec39 | MATLAB | 1,492 | 44 | %% pairedResample
%
% Used when we have paired data which we are 'resampling'; ensures that the
% shuffle points which are randomly drawn from one group matches the other
% groups EXACTLY.
%
% Returns a tensor of the observations for later manipulation;
%
% Assume data is a [nObservations x nGroups], with eac... |
609c33bfe1f0131acc9755e03a0367f39dc706abe6fd0606dca66198190e0d2f | MATLAB | 1,492 | 45 | function out = spm_run_fmri_data(job)
% Set up the design matrix and run a design
% SPM job execution function
% takes a harvested job data structure and call SPM functions to perform
% computations on the data.
% Input:
% job - harvested job data structure (see matlabbatch help)
% Output:
% out - computation res... |
aa792151df2ff7120b765d20b6fe2dfb98f606457d63544e46d58c1a99f9be33 | MATLAB | 1,492 | 76 | function out = wwhich(s1,s2)
% Like built-in which but supports wild cards
% Locate m-files using wildcards
% Works exactly as WHICH, but you can
% use wild cards.
%
% out is a cell whenever 2 or more
% matches are found or if the flag
% -all was used
%
% Note: a function may be shawdowed,
% ... |
aae583f8286c38fd1688fcc3f7ff0d681b21bc1436aacecd0b6f0624fd259da6 | MATLAB | 1,492 | 20 | % SOURCE
%
% Files
% angauss - Anisotropic gaussian filtering.
% cropt - Crop a tomogram, set to zero voxels in the border of the tomogram
% diff2d - Differentiation in 2D images
% diff3d - Calculates partial derivative along any dimension in a tomogram.
% dtvot... |
ee67771af66be4d7121e7d1dd804cd3b879ecce76648414b354ccd514c2918f7 | MATLAB | 1,492 | 47 | function mergedTbl = tableAppend(tbl1, tbl2)
% mergedTbl = tableAppend(tbl1, tbl2)
% tbl1 - Main table to which tbl2 will be appended. This table will be
% unmodified.
% tbl2 - Table that is being appended. Only the variables that are present
% in tbl1 will be conserved.
%
% mergedTbl ... |
eff597d44af3620a388d4ec8b98869f36d0bd8a730e92c3901523047871b3ce7 | MATLAB | 1,492 | 61 | function [ stat_mean stat_dev stat_sem ] = ...
wlStats_getBootstrappedStats( datavals, bootcount )
% function [ stat_mean stat_dev stat_sem ] = ...
% wlStats_getBootstrappedStats( datavals, bootcount )
%
% This computes the mean, standard deviation, and standard error of the
% mean for a set of samples. SEM is est... |
7d0a4404c6c08eb4ae419d8fcee48ff01bc57aa540d27d278186068e26343ba7 | MATLAB | 1,493 | 50 | function [Q] = VBA_spm_Q(a,n,q)
% returns an (n x n) (inverse) autocorrelation matrix for an AR(p) process
% FORMAT [Q] = spm_Q(a,n,q)
%
% a - vector of (p) AR coefficients
% n - size of Q
% q - switch to return inverse autocorrelation or precision [default q = 0]
%___________________________________________________... |
855af7e3c1840c81a5ab0e7eb105ee875514d010b0bc964ecbed517ca272544d | MATLAB | 1,493 | 36 | function [gx] = g_wrap_perseveration(x,P,u,in)
% wraps observation function to include (anti-)perseverative bias
% function g_wrapInGame(x,P,u,in)
% A perseveration bias occurs when an agent tends to repeat his past
% action, irrespective of his beliefs and/or preferences. It can be
% modelled as a bonus for repeating ... |
89aac44760a744bec985ff8bb0db1450c59bab003348647430b8d4ceb37c32bb | MATLAB | 1,493 | 46 | function clf = clfEcoc(p,clfInit,clfparams,nclasses,use01targets)
% Wrapper for ecoc that makes ecoc compatible with nfoldxval.
%
% Requires the SVM toolbox by Anton Schwaighofer.
%
% USAGE
% clf = clfEcoc(p,clfInit,clfparams,nclasses,use01targets)
%
% INPUTS
% p - data dimension
% clfInit - bi... |
0afab900b14c7fae29e62e40c390769d69bcbc3afb407be1103d89bf2434e53e | MATLAB | 1,494 | 44 | function [ rawmag, rawfreq, rawphase ] = ...
wlProc_calcAnalytic(data, samprate)
% function [ rawmag, rawfreq, rawphase ] = ...
% wlProc_calcAnalytic(data, samprate)
%
% This function uses the Hilbert transform to generate an analytic signal
% for the specified input signal, and from that extracts magnitude and ph... |
12f11db54ef08e1e6bf95a27e724374d378ff0137c1bc6657f6b9f068f11184f | MATLAB | 1,494 | 49 | function y=odd(x);
%ODD Round towards nearest odd value.
% Y=ODD(X) rounds each element of X towards the nearest odd
% integer value. If an element of X is even, ODD adds +1 to
% this value. X can be a scalar, a vector or a matrix.
%
% X : scalar, vector or matrix to be rounded
% Y : output scalar, vector or matrix c... |
21b42c4d1d9d8ec470dd3c4127d2606783159b1140e13d6c2a3ad0fdf0e52d85 | MATLAB | 1,494 | 38 | function [fx] = evolution0bisND(x,theta,u,in)
% 0-ToM's evolution function (without doubled hidden states)
% function [fx] = evolution0bisND(x,theta,u,in)
% 0-ToM is simply tracking the log-odds of P(o=1), where o is the
% opponent's action. This variable is updated according to a Laplace-Kalman
% filter, yielding 2 su... |
8e3cc30705720cbaac62a16ad25f22ce1257cec98ef8ed309dc6cc5171de6947 | MATLAB | 1,494 | 52 | % Compute unigrams and bigrams of Darwin's "On the origin of
% species". Written by Matthew Dunham
close all;
verbose = 1;
fid = fopen('darwin.txt');
if(verbose),display('reading file...'),end;
data = fread(fid);
if(verbose),display('done'),end;
fclose(fid);
lcase = abs('a'):abs('z');
ucase = abs('A... |
d3ad4168545ea9006d4d827e8007facefe3f93e631d4c43068fcbc4e1023a0d0 | MATLAB | 1,494 | 60 | function [k,g,s,time,Ck] = vdSpiralDesign(Nitlv, rv, res, fov,radius , Gmax, Smax, T,ds, interpType)
% [k,g,s,time] = vdSpiralDesign(Nitlv, res, fov,radius , Gmax, Smax, T, interpType)
%
% This function designs a variable density spiral
%
% Input:
% Nitlv - Number of interleves
% rv/riv - Indicates type of s... |
ddda7a0584fb83e8fdd41ce222fae300af650bb5a01c8b9e6d9fe322022e6c44 | MATLAB | 1,494 | 39 | %% Perform a random walk on the integers 0:20
% Visualize the probability of the the states for various time steps,
% and different initial conditions.
%%
% This file is from pmtk3.googlecode.com
function randomWalk0to20Demo
T = diag(repmat(0.5, 1, 20), -1) + diag(repmat(0.5, 1, 20), 1);
T(1, 1) = 0.5; T(21, 21) = 0.... |
fcb36fc491f22b3c0c9b28244f84329ddd8daddf32a940870850637714b7a818 | MATLAB | 1,494 | 73 | function [center,radius]=sphfit(vc)
% fits a sphere to a set of surface points
%
% input:
% vc nx3 matrix, where each row represents the location
% of one surface point. vc can have more than 3 columns
% (e.g. orientations) - then only the first 3 columns are used
%
% center 1x3 vector denoting the cente... |
077f7a541303236ea9cc3ab42bcf427dd11c7467580f28424cd4f81bbfc5e716 | MATLAB | 1,495 | 52 | function FD_jenk = CBIG_ABCD_proc_compute_FD_Jenkinson(motion)
% FD_jenk = CBIG_ABCD_proc_compute_FD_Jenkinson(motion)
%
% This function compute the FDRMS (Jenkinson) from the 6 motion parameters
%
% Inputs:
% - motion:
% #frame*6 matrix. The 6 motion parameters. The first 3 should be rotation in radians, the ... |
282c989a34574940b02b283a560361976008a0ed4e50088b5ad42b1268fee969 | MATLAB | 1,495 | 40 | function prec_apply_deform(input_fn,ref_img,y_fn)
for i = 1:numel(input_fn)
[filepath,name,ext] = fileparts(input_fn{i});
mask_icv = ['mask_icv_',name,ext];
mask_bg = ['mask_bg_',name,ext];
matlabbatch = {};
matlabbatch{1}.spm.util.defs.comp{1}.def = {y_fn{i}};
matlabbatch{1}.spm.util.d... |
cb3a90cd3b413d37517a8bbad1083cdc02f31a6d6483f4c8133b5acbcbd88615 | MATLAB | 1,495 | 91 | function loc_phys=mk_coordinates_highlevel(mnt,pars);
inds=1:length(mnt.x);
inds=inds(isnan(mnt.x)==0);
sensors=[mnt.x(inds),mnt.y(inds)];
[ns_ori,ndim]=size(sensors);
if nargin>1
if isfield(pars,'rot');
rot=pars.rot;
else
rot=0;
end
if isfield(pars,'nin');
nin=pars.nin;
else
nin=n... |
eb54ff8f33ee79beeb0f076c35daa96f6b224fd7c09705ddd2f6028cc3470f15 | MATLAB | 1,495 | 63 | clear;close all;clc;
foldername='Lin24';
secv=[50,100,200,400,600];
sigma=linspace(1,100,200);
y2=-100:99;
x2=-100:99;
[X,Y]=meshgrid(x2,y2);
mainfolder=cd(foldername);
for j=1:length(secv);
No{j}=num2str(secv(j),'%05.f');
filename=['t=',No{j},'.png'];
a=imread(filename);
b1=double(a(:,:,1... |
44127058b9c33c9873d914c62c51f1982a2b55bd31145c41d19ac379f55a9d3e | MATLAB | 1,496 | 41 | function B = assignToBins( A, edges )
% Quantizes A according to values in edges.
%
% assignToBins replaces each value in A with a value between [0,nBins] where
% nBins=length(edges)-1. edges must be a vector of monotonically
% increasing values. Each element v in A gets converted to a discrete
% value q such that ed... |
7d865dcc01329b41f5407357299de40541c99269dd77dd90ded324f80cc5a955 | MATLAB | 1,496 | 37 | function [u,options,dim] = addConfounds2dcm(X0,u,options,dim)
% this function modifies the i/o of DCM inversion to cope with confounds
% function [u,options,dim] = addConfounds2dcm(X0,u,options,dim)
% This function adds in a dummy input that indexes time, which is used in
% the observation function of DCM to extract th... |
f48ceeade9f5f3b8d0840cbb3542739414985d098c37465b09fd103935fd76b9 | MATLAB | 1,497 | 57 | function [gotTrigger, timeStamp]=waitForTrigger(syncBoxHandle,triggerN,timeOut)
%
% waits for timeOut seconds for the Nth MR trigger on port
%
% Example usage:
% waitForTrigger (syncBoxHandle, 1, 300)
%
% Inputs:
% syncBoxHandle (handle) - handle to I/O port
% triggerN
% timeOut (int)
% Out... |
fc73edf989080c6801ae5ad77b2c9f05b6318fdb7a50442cb7d69e191075d402 | MATLAB | 1,497 | 62 | % Plot stimulus-locked mean traces for all coherences - considering nans in
% each trial
% meanTracesSL_bigSbigT
if exist('sigSL') == 0 && exist('normS') >= 1
sigSL.sig_coh = normS.sigSL.sig_coh;
sigSL.t = normS.sigSL.t;
elseif exist('sigSL') == 0 && exist('normS') == 0
error('No signal struc... |
fde0ec2d55c11f7fae4d8547856af0564db768b589dc74d1a5341b79f21fa6fd | MATLAB | 1,497 | 64 | function TF = exists(path, dir_only)
%EXISTS Returns true if the specified path exists in the filesystem.
% Usage:
% TF = exists(path)
% TF = exists(paths)
% TF = exists(_, dir_only)
%
% Args:
% path: string path
% paths: cell array of paths or scalar structure where fields are paths
% dir_only: if true, re... |
05b70fe500cd16cc9e94f8ea644d4c51880e7f514188bede219ccb9fb5e7b244 | MATLAB | 1,498 | 58 | % 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 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
4345f381d3c56badae389c0068b1039a8c167fb9f1f7edc426fa54022a8c88e8 | MATLAB | 1,498 | 58 | % 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 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,... |
888a6117095c6b0fa51faa4ede4ae17867cb0eda875db6059d9aca0080b75de1 | MATLAB | 1,498 | 50 | classdef SortedStringMap < handle
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Provided by the Herzenberg Lab at Stanford University
% Lice... |
629c3a659a40225dbb1e57722202cf5b603c815720b889d67ba9c5c9b8b67e0e | MATLAB | 1,499 | 54 | function plot_fourierp(LAN,nch,t)
% <*LAN)<]
% PLOT_FOURIERP do a plot of FT of the channel 'nch' and the trials 't'
% plot_fourierp(LAN,'Cz') Do the mean od the electrode Cz
% plot_fourierp(LAN,[ 10 11],5) Do plots of the 5th trial for the
% electrodes number 10 and 11
%
% v... |
70230a2167c14d6bdf41c4cdd93f4b5c211e16ecc5e36d9ec9b6611ee3856690 | MATLAB | 1,499 | 44 | %function converts python outputs of suite2p into mat files for any number
%of planes
function [] = suite2p2mat(mousefolder, nplanes)
% mousefolder = the directory where the suite2p folder is found
% nplanes = the number of planes in the suite2p folder
for i=1:nplanes;
d = [mousefolder '\suite2p\plane' num2s... |
976839c591bde9a24757defa0db5a3be14403dcc01c12855b23b6ee55dced020 | MATLAB | 1,499 | 92 |
if ~exist('I_1'),
active_images_save = active_images;
ima_read_calib;
active_images = active_images_save;
check_active_images;
end;
check_active_images;
if isempty(ind_read),
return;
end;
n_col = floor(sqrt(n_ima*nx/ny));
n_row = ceil(n_ima / n_col);
ker2 = 1;
for ii = 1:n_col,
ker2 = conv(ke... |
adb4de4554e95eaaced2f50f33d680f1b2d49a0b0fd98c2da87f87953895a746 | MATLAB | 1,499 | 44 | function[mean_aligned_activity, aligned_activity, cell_id] = grab_lap_activity(analysis_out, samples, measure, grab_lap, range)
session_names = fieldnames(samples);
initiation_id = {};
region_lap = {};
norm_region_lap = {};
idx = 1;
id = [];
roi = 1;
frame_count = -1000:100;
for session = 1: length(sessio... |
b65109afbcefb993a496a1b0c72e142af3e9952ec0d292e1782be2341680a214 | MATLAB | 1,499 | 31 | function [multi_event_percent multi_event_number] = calculate_multitrack_event_percentage(session_index,event_index,track_1_index,track_2_index)
%
for session = 1:length(session_index)
multitrack_event(session) = sum(ismember(event_index(track_1_index(ismember(track_1_index,session_index{session}))),...
e... |
e8b96b2ee9ea5ff76147a7d2b41055f5584dd7727add94efdcbb98b3c395299e | MATLAB | 1,499 | 58 | function write_nodelm_poly2d(fn,e,p,nodemap,holes)
% Writes the 2D boundary defined in e and p to .poly file format.
% Note that it will create a .poly and a .node file.
% holes is a cell of n by 2:
% holes(:,1) : coordinaets of a point inside the region
% holes(:,2) : material/attribute ID for the hole.
if ~((size(e,... |
f648c5ae3cf105c5cc08c89af6f4b62db1b895034577e2b7e48dc0800f5e528a | MATLAB | 1,499 | 40 | function [DM, xd] = ft_preproc_online_downsample_apply(DM, x)
% function [DM, xd] = ft_preproc_online_downsample_apply(DM, x)
%
% Passes signal x (channels times samples) through the downsampler.
% Returns updated downsample model (numSkip!) and downsampled signal.
% Copyright (C) 2010, Stefan Klanke
%
% This file is... |
84355481b16662242ebae500a5f0fc42026176f6832059e16e522ccea63c76a5 | MATLAB | 1,500 | 55 | function is_same = compare_tif_images(srcDir, dstDir, avgErrTol, postfix)
srcFiles = dir(fullfile(srcDir,['*', postfix, '.tif']));
dstFiles = dir(fullfile(dstDir,['*', postfix, '.tif']));
if length(srcFiles) == 0
disp('no tif file.');
is_same = false;
return;
end
if length... |
8d39653011252f6ee06c9f86de13e2f3707fe9c41f45dfea95cbdec7eaa78460 | MATLAB | 1,500 | 49 | function [model, logev] = linregFitEbNetlab(X, y, pp)
% Empirical Bayes linear regression using Netlab's evidence procedure
% X is n*d, y is d*1
% Do not add a column of 1s
% This file is from pmtk3.googlecode.com
pp.addOnes = false; % netlab already does this
[model.preproc, x] = preprocessorApplyToTrain(pp, X);
ta... |
b22a9bde2fa9849594025b51172ca31a5dfdd12fe7e26d461f555a6cd5137414 | MATLAB | 1,500 | 35 | function candoit = canGetGradient(problem)
% Checks whether the gradient can be computed for a problem structure.
%
% function candoit = canGetGradient(problem)
%
% Returns true if the gradient of the cost function can be computed given
% the problem description, false otherwise.
%
% See also: canGetCost canGe... |
fea56be1258c482529adbbaaa1e2c403cc2cb4d2b762eff9d93f8f89d2ce4e99 | MATLAB | 1,501 | 57 | function h_zStackQuality3(handles)
[currentInd, handles, currentStruct, currentStructName] = h_getCurrendInd3(handles);
maxProjection = get(handles.maxProjectionOpt,'Value');
maxProjectionEnable = get(handles.maxProjectionOpt,'Enable');
if strcmp(maxProjectionEnable,'off')
maxProjection = 2;
end
[xlim,yl... |
13a488e2755b3f63c75f265754b335c53c8d594adf4ad3cf7efe91b278852309 | MATLAB | 1,502 | 56 | function [color, eraseMode, lineWidth] = h_getColor3(synapseAnalysis)
if ~(synapseAnalysis.isLast>0)%unassigned is -1
ROIType = synapseAnalysis.synapseStatus;
else % if isLast has been assigned and is larger than 1.
switch(synapseAnalysis.synapseStatus)
case {'new'}
ROIType = 'transi... |
2c32deb03ab766d33855c6a09f8476baa404d4c5093acf25d6b9c24998051c8f | MATLAB | 1,502 | 45 | function [gx] = g_metaToM(x,P,u,inG)
% observation function for meta-learner (k-ToM vs sequence)
% function [gx] = g_metaToM(x,P,u,inF)
% The meta-learner bases her decision (a=1 or a=0) upon her prediction of
% her opponent's next move, given the game payoff table. The specific
% difficulty of the meta-learner is that... |
3719a665d07bb6e22d8e6a0e5ff2f566f98d692e46f979f62d9f072cff7751d9 | MATLAB | 1,502 | 52 | function rz = getrunningpulses2(rotf,thresh,k,n,fig)
% rz = getrunningpulses(rotf,thresh,k,n,fig)
% This function generates pulses corresponding to running blocks.
% Inputs: rotf = rotary function; thresh = the threshold for generating
% pulses; k = the length of sliding window for movstd, moving standard
% deviation; ... |
681b8faf67e8462c0fefebd7aea79dfe2416987a234100cc657075eb32245c7e | MATLAB | 1,502 | 41 | function generateSynopsisTable(directory, outputFile, rootDir)
%% Create an html table of files and one line descriptions for a directory
% PMTKneedsMatlab
%%
% This file is from pmtk3.googlecode.com
if nargin < 2, outputFile = ''; end
files = filelist(directory, '*.m', true);
files = files(sortidx(low... |
732917f317bbf45c07c5d9cf3a979516c54a12e23e573be548fd84b41c9c5ee8 | MATLAB | 1,502 | 55 | function G = filterDog2d( r, var, order, show )
% Difference of Gaussian (Dog) Filter.
%
% Adapted from code by Serge Belongie. Takes a "Difference of Gaussian" -
% all centered on the same point but with different values for sigma. Also
% serves as an approximation to an Laplacian of Gaussian (LoG) filter (if
% order... |
8868afb164abc7cdef9f4346670d999ea68b796fb7d17642ee68c44b78f6e3f6 | MATLAB | 1,502 | 41 | function r = get_random_sites(sample_size,arena_L,arena_shape,return_as_xy_coords)
% returns r with size(r) == sample_size
% where each entry is a lattice site in the arena grid of shape arena_shape
% each entry in r can be translated to an arena x,y-coordinate by using func.myind2sub([L,L],r,true)
% if return_as_xy_co... |
5444330a9043c994180ce0a42aad6d7a76f97b16afe73897685aec0e8d5f1b7d | MATLAB | 1,503 | 39 | function [rm, names] = fs_get_rm(subpath, annot_name)
% Combine rh and lh .annot file
% Input subpath:subject path
% annot_name:annotation file name
[~, label1, colortable1] = freesurfer_read_annotation([subpath '\lh.' annot_name '.annot']);
[~, label2, colortable2] = freesurfer_read_annotation([subpath '\rh... |
76c2d04e8c3fc47293eea8d5bd4f5eb646e13307803524819dac0f32c8160593 | MATLAB | 1,503 | 36 | clear all
%%
%Define Parameters
[opt] = ParameterOptions();
%%
%Generate Pathway Amplitude & Gradient Waveform basis set
%First Dictionary
[PathwaySignalFirstOrder,GwaveFirstOrder,TransFirstOrder] = PathwayOperatorOrder(opt,'First');
%Second Dictionary
[PathwaySignalHigherOrder,GwaveHigherOrder,TransHigherOrder] = Path... |
c43a4dcc2181339098d0bab7256f6d6bdcfed618b77019b40b0909f4bc3ac6db | MATLAB | 1,503 | 42 | % normalization
function success_code = normalization()
loadParameters;
% Removed the formal requirement for four channels. -DG 2020-09-09
%if length(params.SHIFT_CHAN_STRS) ~= 4
% disp('# of channels is not 4.')
% return
%end
arg_list = {};
postfix_list = {};
run_num_list ... |
f123b41c61e64fbd83518cd5aba88122fd84e09732476a746bf04705dec8cd9b | MATLAB | 1,503 | 53 | function [Xtrain,ytrain,Xtest,ytest] = setupMnist(varargin)%binary, Ntrain, Ntest,full)
% Load mnist handwritten digit data
% Optional arguments [default in brackets]
% binary - if true, binarize around overall mean [false]
% ntrain - [60000]
% ntest - [10000]
% keepSparse - if true, do not cast to double [true]
% clas... |
a3d3f4aa5f1b7a6b34c6641e0ef06db06560e5d6fd6a851a9be1bd043148f12f | MATLAB | 1,504 | 72 | function data = ReadChoreDatFile(filename)
nparams = 7;
data = [];
fid = fopen(filename,'r');
if fid < 1,
error('Could not open file %s for reading',filename);
end
ids = [];
expname = '';
while true,
l = fgetl(fid);
if ~ischar(l),
break;
end
if isempty(l),
continue;
end
% first word is the ... |
ed4b274e2557aff00257f1a06a6892e4a8cae82c999a1c4831b3e7751f71f2b2 | MATLAB | 1,504 | 54 | function h = SuperimposeKS(data, ksArgs, yMinMax, colour, alpha)
% function SuperimposeKS(data, ksArgs, yMinMax, colour, alpha)
%
% Superimpose a KSDensity of a distribution (e.g. RT) onto a figure.
%
% Inputs:
% data = data to run ksdensity() on. Will convert to column first
% ksArgs = cell array of arguments pa... |
efe728cb08e57e888be13ff8db81f4cfd1c58bb7aa78f70f9446b001f2771104 | MATLAB | 1,504 | 32 | % 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 the ... |
20b650683823435e4d12f03b84d969634aa33c616e5c3c0b9c0d531e2375a353 | MATLAB | 1,505 | 50 | %% Visualize the Projection of 3D Gaussian Ellipsoids onto the 2D Plain
%
%%
% This file is from pmtk3.googlecode.com
C = {[2 4 10] [12 0 10] [20 0 10]};
R = {[6 3 3] [3 6 3] [3 3 6]};
npoints = 25;
nellipsoids = length(C);
D = repmat(createStruct({'X', 'Y', 'Z'}), 1, nellipsoids);
f1 = figure; hold on;
colors = pmtk... |
7f7c08dee9c243d407a534b59c5484d3333e7de92915b48aa7f8c91a45b0a978 | MATLAB | 1,505 | 46 | function vert = forceVert(im,im_ecc,im_pol,ecc,pol,varea,area_val)
%{
Occasionally, no vertices will be found when you want them to be when
binary is true. This function will find the single vertex nearest the
centroid of the object in the image. As of now, this assumes there is only
up to a single object per hemifield... |
7e2231139253d63fd1372fa55c4203b6802bfc1b62f0d326eb5f0c86566e3bcb | MATLAB | 1,506 | 46 |
%% general options
elec_path = fullfile(patient_path,'dipoles',strcat(patno,'_',model_name,'_', ...
dipole_name,'_electrodes.mat'));
%% load BEM-FMM Engine
addpath(fullfile('../engines/bem_fmm_engine'));
%% load skin shell
skin_id = find(strcmp(tissue,'Skin'));
... |
9dfef6d7344bdbc2f2a494623e8234d02aa1e440210c7d8091a860dfe259c4a0 | MATLAB | 1,506 | 47 | disp("Perf and math test matlab driver for FMM3D/Stokes")
disp("Source to target, stokeslet+stresslet (1-vec), vel pot only...");
% Barnett 8/4/23
clear
ns = 100000;
nt = 100000;
eps = 1e-3;
ifstrs = 1; % include stresslets?
ifppreg = 0; % no eval at sources
ifppregtarg = 1; % just vel out
rng(0)
srcinfo.... |
ef2eca5dc02b891802165bc536b8b91c1f954175947993db4d81f8039069e5f1 | MATLAB | 1,506 | 43 |
data = dir('/DATAPOOL/ERRORMONITORING/SEM_mri_data/P*');
%%
sub = 1;
for i = 1:size(data,1)
fprintf(data(i).name);
data_func = dir([data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/nifti/func/run*']);
data_anat = [data(i).folder, '/', data(i).name, '/mri/SEM_', data(i).name, '/n... |
f266e1dfb8f6314fdd7b8478c12c134b5bac12a5895d2ad63780f20b101d0dad | MATLAB | 1,506 | 50 | function [matdif, ParElec] = difphaser3(matphase, step)
% [matdif, ParElec] = difphaser3(matphase, step)
% Computes the phase diferences between all the electrode pairs, provided
% in a matrix of phase info. (Output of sinwave6)
%
% INPUT
% matphase : 3D Matrix of phase information. 1D electrodes, 2D timepoin... |
87b4efd618cb6dff166daa674e7f28ecd968ea19627277413c03fe6c54faa561 | MATLAB | 1,507 | 66 | %% Kmeans Model Selection in 2D
%
%%
% This file is from pmtk3.googlecode.com
setSeed(0);
d = 2; ncentres = 3;
mix = gmm(d, ncentres, 'spherical');
mix.centres = [1 1; -1 -1; 0 0]; % mu(k,:)
mix.covars = [0.1 0.1 0.1];
n = 1000; ndx = 1:n;
Xtrain = gmmsamp(mix, n);
n = 1000;
Xtest = gmmsamp(mix, n);
figure;
%Ks = [... |
81cc3ac4960aece54df42391747a579146f2b270fcef2e7af3271ac7243b70f4 | MATLAB | 1,508 | 41 | function [tc,nodes,status]=FixPatchOrientation(p,sfaces,meshnodemap,silentflag)
% [tc,nodes,status]=FixPatchOrientation(p,sfaces,meshnodemap)
% Assuming the 3D shell defined by p and sfaces is a closed one, this
% routine will make sure that all the facets are pointing outward.
status=0;
if nargin<=3 || silentflag==0
... |
a5f560111909578c3225c7ed6aec404bb7dcab8368ce09fd574ca72f02c51d39 | MATLAB | 1,508 | 43 |
function Output_Image_RGB=ColorMasking(Input_Image_RGB,Mask,OverlayColor)
if size(Input_Image_RGB,1)~=size(Mask,1)||size(Input_Image_RGB,2)~=size(Mask,2)
warning(['Input Height = ',num2str(size(Input_Image_RGB,1))])
warning(['Mask Height = ',num2str(size(Mask,1))])
warning(['Input ... |
e0829ac70dd2ca39b8d135518db32ec82485671d33a19bb719e7892f43e614a3 | MATLAB | 1,508 | 48 | %%Used to divide behavior into different planes for each imaging plane
% Chad Heer; Sheffield lab
function [] = splitplanes(behavior_file, sbxframes, nplanes, outfilename)
%behavior = unsplit behavior data (output of loadbehshef)
%sbxframes = vector with the number of frames for each sbx file
%nplanes = number of ... |
e52d5e2fd7d3712434adec61c48499999ffc68b68f6ddf992282e2b65292b10e | MATLAB | 1,508 | 58 | function [SWI, C, L] = calcSWI(W)
% CALCSWI calculates the Small-World Index of a connection matrix.
%
% Inputs:
% - W: Connection matrix (weighted or binary)
%
% Output:
% - SWI: Small-World Index of the matrix
%
% References:
% Neal et al., 2017
% https://www.cambridge.org/core/services/aop-cambridge-core/content... |
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