sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0687eaff1089cbd6b4c17eb0a713412f82286bd52a048ff524eeb5c955a11e86 | MATLAB | 705 | 31 | function profile_end(profile_on, profile_dir)
if ~exist('profile_on','var'), profile_on = 0; end;
switch profile_on
case 0,
ptime(toc)
case 1,
ptime(toc)
if str2num(strtok(version,'.')) > 6
% profile off
if ~exist('profile_dir','var'), profile_dir = 'profile'; end;
profi... |
23d64a9fc3a0b24ee9b047188aa2a48ce8fc5c70bb45cca0a5ca130747ce5d99 | MATLAB | 705 | 36 | function setOut = fisherTransform(setIn, fakeIt)
% Computes a Fisher Transformation on the input vector
%
% USAGE:
% setOut = fisherTransform(setIn[, fakeIt])
%
% (setting fakeIt to true will replace inf values by 1/eps)
%
% Cai Wingfield 2-2010
%_______________________________________________________________________... |
32bc0df4d67e8529b758c3c39a6954c7c6947fb53465f4d479e4b1341886a732 | MATLAB | 705 | 35 | function r = mtimes(p,q)
%TIMES this function multiplies the x, y, and z values of the structures that I use in
% the FVtool.
% reassign the scalar to new variable a and the struct to new variable b
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALSO:
%
% Copyright (c) 2012-2016 Ali Akbar Eftekh... |
983148e6e06c64ea0d19403e3f9c8c636b6bbfe8fa0644e1f086d121148dfe1a | MATLAB | 705 | 25 |
%
dicome_header = dicominfo(['/Users/bo/Desktop/' ...
'MRI_examplar_image/bold/sms_bold_run1-00001.dcm']);
slice_timging = dicome_header.Private_0019_1029;
slice_timging = slice_timging * 0.001;
slice_timging = slice_timging/2;
%
dicome_header = dicominfo(['/Users/bo/Documents/data_liujia_lab/analysis_liuP1_g... |
b220011cf1486c699c6ddd5e2c1db6880a23ef844bf7264a7aa5d12d0345b2c6 | MATLAB | 705 | 23 | function reader = getReader(key)
% Returns reader object for key. Key can be a key struture or
% any relvar where fetch(rf.Align & key) returns a single tuple.
if ~isstruct(key)
key = fetch(rf.Align & key);
end
assert(length(key) == 1, 'one scan at a time please')
% Fetch path and basename from TpSession and Tp... |
44a56eff871376d6dfa10f7f891d0b9f83b8f6c5c05d83f3bca4275416027b2a | MATLAB | 706 | 20 | function plot_amp_ncc(rez,i)
Spike_id = find(rez.st(:,end)==i);
Nchan = length(cell2mat(rez.Merge_cluster(i,5)));
%Get histogram of spikes amplitudes
amplitudes = rez.st(Spike_id,5);
[Ncount,edgesS] = histcounts(amplitudes);figure;
subplot(1,2,1)
bar(edgesS(1:end-1),Ncount(1:end))
... |
44bf7e51d6d0e35ca0ccfda1f914518714e5138306a60bf1be38e0bdea8a45c5 | MATLAB | 706 | 26 | function keyCode = detectkey(params)
%DETECTKEY checks if there is an input either from the keyboard or form the
%response box
%
% Inputs:
% params: data storage file
%
% Outputs:
% keyCode: vector of numbers corresponding to the pressed keys
%
% About:
% Coded by F.Petzschner 19. April 2017
% Last change: F.Pet... |
79058eb4dfc64217ddd2b55003c888db3a87bb208de5a09be402e47e0fb92dc4 | MATLAB | 706 | 15 | function vers = eegplugin_viewprops( fig, try_strings, catch_strings )
%EEGLABPLUGIN_POP_PROP_EXTENDED View extended channel/component properties
% Displays ERPimage, spectopo, topomap, activity scroll, dipole, and pvaf
vers = 'ViewProps1.5.4';
if nargin < 3
error('eegplugin_viewprops requires 3 arguments');
end
... |
84a0b002a163609e0636b958a35efddf7dbb9f5675ac3154b9178395f3300be8 | MATLAB | 706 | 25 | function [CPInByRewMean, CPInByRewSEM] =...
DA_CPInByReward(pdata, bdata)
% DA_CPInByReward - average photometry response by reward in mixed blocks
% INPUTS:
% pdata - photometry data
% bdata - corresponding behavioral data
% OUTPUTS:
% CPInByRewMean - mean response
% CPInByRewSEM - SEM response
% Prealloc... |
d606e118f9fc2a3ddd0deb95d9bbb5511476941109e53798113f35c0ca58c52f | MATLAB | 706 | 50 | function xopt = testhyperbolicmanifold()
n = 10;
N = 5;
transposed = 1;
if transposed % BM: okay
trnsp = @(X) X';
else
trnsp = @(X) X;
end
problem.M = hyperbolicfactory(n, N, transposed);
Y = randn(n+1, N);
problem.cost = @cost;
problem.egrad = @egrad;
problem.ehess = @ehess;
function f = cost(x... |
f9d6735b6c456a08ce90adb5c4392297ff1d266080d8d624cdced6528047e2ce | MATLAB | 706 | 23 | function tapas_BLT_runEnd(params)
% tapas_BLT_runEnd ends the task and stores and close everything
if params.doMRI == 1
% Show preliminary end screen for the duration of the field map
Screen('DrawTexture', params.screen.window, params.text.endfieldmap, [], params.screen.fit, 0);
Screen('Flip', params.scre... |
ddbe5121c70241e7b66bd4d92a4d92df08d7e52cb80429268da008bd3fef0c4f | MATLAB | 707 | 26 | function varargout = covPERard(varargin)
% Wrapper for PERiodic covariance function covPER.m.
%
% Periodic covariance function from an arbitrary covariance function k0 via
% embedding IR^D into IC^D.
% The covariance function is parameterized as:
%
% k(x,z) = k0(u(x),u(z)), u(x) = [sin(pi*x./p); cos(pi*x./p)]
%
% wher... |
2429de68f887da33dae09b15bf2612038073507c85e3faf7cc5ad9461fa8aabf | MATLAB | 708 | 33 | function colors = niceColorsWarm2(Ncolors)
% just a simple one-liner to produce up to 4 colors for plotting. Uses
% predefined colors from a nice figure in a paper
if nargin == 0
figure; meansembarFigure(rand(6),'color',niceColorsWarm2(6))
return
end
if Ncolors > 6
error('Only 6 colors implemented')
end
dark... |
33475e63732ae3e5b1c5f3bf0e9687e0c864742a2315c7d10e208efbf10630e2 | MATLAB | 708 | 15 | function outdata = Switch_MergeExperiments(indata,pairedsessions,experimentID,mergesides,sideindex)
outdata = indata;
if mergesides
dimsize = ndims(indata);
outdata = permute(outdata,[1 sideindex setdiff([2:dimsize],sideindex)]);
outdata(experimentID==2,1,:,:,:,:,:,:,:,:,:,:) = mean(outd... |
6063ffbc768dfc63965fc2a3e8537d6abb7405efe763e5e18d1433ed42ea08ae | MATLAB | 708 | 17 | function R = loadCombinedDataset(dataset, dataPath)
% Loads two datasets from the same mouse and combines them
mouse = dataset{1}{1};
session1 = dataset{1}{2};
session2 = dataset{1}{3};
% First
[R1, ~, ~] = loadData(mouse, session1, 'R', 'DLC3', dataPath);
% Second
[R2, ~, ~] = loadData(mouse, session2, 'R', 'DLC3', d... |
ae5fe8a6eae910247bc1b05c7a052fa92b660f4b2df6418da9bd004f20ccb282 | MATLAB | 708 | 24 | function out = vl_nnsigmoid(x,dzdy)
%VL_NNSIGMOID CNN sigmoid nonlinear unit.
% Y = VL_NNSIGMOID(X) computes the sigmoid of the data X. X can
% have an arbitrary size. The sigmoid is defined as follows:
%
% SIGMOID(X) = 1 / (1 + EXP(-X)).
%
% DZDX = VL_NNSIGMOID(X, DZDY) computes the derivative of the
% blo... |
ce076ea95047ca0a54c72b38c7c6d6f0e8eb179870bc78e1dfab16f809e8486f | MATLAB | 708 | 23 | function varargout = covSEiso(varargin)
% Wrapper for Squared Exponential covariance function covSE.m.
%
% Squared Exponential covariance function with isotropic distance measure. The
% covariance function is parameterized as:
%
% k(x,z) = sf^2 * exp(-(x-z)'*inv(P)*(x-z)/2)
%
% where the P matrix is ell^2 times the u... |
45e5f8e4d1bb8bcef4de828ab4d4ed38b20623a6e2499be93f3a963c6165335c | MATLAB | 709 | 23 | function params = preprocColorSpace_GetMetaParams(argNum)
params.class = 'preprocColorSpace';
switch argNum
case 1
% Convert to L*A*B colorspace, keep luminance channel
params.class = 'preprocColorSpace';
params.colorconv = 'rgb2lab';
params.colorchannels = 1;
params.gamma ... |
482822dd591032ab4cbde9d0570a993ce9e63108d6a3b083ce6b100e68fb1064 | MATLAB | 709 | 30 | % Computes (unnormalized) cross-covariance function out to +/- L lags
% (TR shifts) between each column of Avg1 and Avg2
% Avg1 and Avg2 are time x region matrices/vectors
% See tdmx_template.m for appropriate normalization of lagged_cov output
function r = lagged_cov(Avg1,Avg2,L)
L1 = size(Avg1,2);
L2 = si... |
5b8516c92e345759305250296fa67044cbf0b28907e888297db7a39d50ca8933 | MATLAB | 709 | 26 | load('Spinalgain_EMG_relationship')
figure
for perf = 1:4
dat = emg_para{1,perf}(:);
[N,edges] = histcounts(dat,10);
subplot(2,2,perf), bar(edges(2:end),N./length(dat))
hold on, plot([0.05 1.05],[0.1 0.1],':k')
title([emg_para{2,perf},' ',emg_para{3,perf}])
p_row = ones(... |
7d8baae53a1de0bb2398f96254b6bfecdaee7394b0787a1d65645b1427d9f101 | MATLAB | 709 | 22 | % Compute the log intensity for the inverse link function g(f) = log(1+exp(f))).
% Output range: 0 <= g(f).
%
% The function can be used in GLM likelihoods such as likPoisson, likGamma, and
% likInvGauss.
%
% Copyright (c) by Hannes Nickisch, 2016-10-04.
function [lg,dlg,d2lg,d3lg] = glm_invlink_logistic(f)
l1pef = ... |
8ddd0fa676d537bdf5c2efdbf39dd5f750c65e8f506571741454731b3af3fde6 | MATLAB | 709 | 35 | %
% Same as sh_layoutLayoutPowerAB but also include the non-oddball trace to
% compare with oddball (e.g. A baseline + B oddball + B baseline)
%
% sh_singleERPcolor(array,epoch,cRange,Fs)
%
% Frg: frequency range to compute the band power
% step: time length to compute the bandpower
%
%
% global ChLayout
% global nB... |
41426248bf6863b1cefe0a9cbceebf3145e727a4728c6712aafc26d55c36b774 | MATLAB | 710 | 21 | data = readtable("filename.csv");
test_data = data(data.freq_band == "beta", :);
% GLME
model = fitglme(test_data, "br ~ period * region + (1|subject)");
anova(model)
% ANOVAN
[p, tbl, stats, terms] = anovan(test_data.br, ...
{test_data.period, test_data.region}, ...
'model', 'interaction', ...
'varnames'... |
469627bcd2f89d9074a1c0376e9289d3a4892e7eba67bd8fe580ce6c53aa1737 | MATLAB | 710 | 42 |
% Panel can incorporate an existing axis.
%
% (a) Create the root panel.
% (b) Create an axis yourself.
% (c) Pack an automatically created axis, and your own axis,
% into the root panel.
%% (a)
% create a column-pair layout, with 95% of the space given
% to the left hand panel
p = panel();
p.pack('h', [95 -... |
75fbed2a9db968b887ae3368cddc18b526f2622729f7dfec7677a8ebd392fdc8 | MATLAB | 710 | 17 | function dphase = tapas_physio_downsample_phase(tphase, phase, tsample, rsampint)
% Author: Lars Kasper, using code from Chloe Hutton (FIL, UCL London)
%
% Copyright (C) 2013 Institute for Biomedical Engineering, ETH/Uni Zurich.
%
% This file is part of the PhysIO toolbox, which is released under the terms of the GNU... |
c1754a746726caa3a7e460f88be395c2fa94978f613165c59c70fe9f142b4cad | MATLAB | 710 | 25 | function [CPIn20ByBlkMean, CPIn20ByBlkSEM] = DA_CPInByBlock(pdata, bdata)
% DA_CPInByBlock - average photometry response by 20 ul across blocks
% INPUTS:
% pdata - photometry data
% bdata - corresponding behavioral data
% OUTPUTS:
% CPIn20ByBlkMean - mean response
% CPIn20ByBlkSEM - SEM response
% Preallocate ... |
c29d21098d333eb13bd3833ba4dafa5dd2e40f19a7607869a74c349b18bfa13f | MATLAB | 712 | 25 | function [ output_args ] = normalisePatternEnumeration( input_args )
%NORMALISEPATTERNENUMERATION( input_args ) Normalised the enumeration of
%the input pattern while keeping the overall pattern unchanged. In the
%enumeration new indices will be added as required.
%
% INPUT:
% input_args [1x? matrix]: input pattern... |
82333ec3b2d3408238d6fa421bc4b14b8153b5d3345d9ad964c873877b9c0516 | MATLAB | 713 | 29 | function hirf=boyntonModel(res)
%returns a vector containing the hemodynamic impulse response function
%as estimated by boynton, engel, glover and heeger (1996) for two subjects' V1.
%the parameter res controls the temporal resolution (time bin width is 1 ms).
%________________________________________________________... |
28244fa0932af08dca6ef3c94947791647ec74cdf3f683e8c4895f284e99cfa7 | MATLAB | 716 | 34 | function faceGrad = gradientTerm(phi)
% this function calculates the gradient of a variable in x direction
% it checks for the availability of the ghost variables and use them, otherwise
% estimate them, assuming a zero gradient on the boundaries
%
% SYNOPSIS:
%
%
% PARAMETERS:
%
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALS... |
48013ca8809cf43e19aac461a892a6ea6d772fa01951ee5fee99b9e203276c50 | MATLAB | 716 | 23 | function Protated = qRotatePoint( P, Qrotation )
% qRotatePoint: rotate a point according to rotation quaternion
% Protated = qRotatePoint( P, Qrotation )
% IN:
% P - point which is rotated
% Qrotation - quaternion describing the rotation (axis and angle)
%
% OUT:
% Protated - rotated point
%
% EXAMPLE:
... |
786cb55bde1e5cb11cd49b9adb18249f6de117056725cc7ebfd1ea4d7e57600f | MATLAB | 716 | 33 | clear all;clc
% open a file to store random factors
for rank=0:49
fname = sprintf('../input/proc_%02d/random.dat',rank);%don't forget the PPT in the file name
fid=fopen(fname,'w');
%fileID=fopen('input/proc/random.dat','w');
%fprintf(fileID,'%6s %10s\n','normal','log_normal');
%rng(0,'twister');
% randn... |
7d483bdcafad774df1f6a39a0653cdfb14f30ab423141dc8182594edfa780373 | MATLAB | 716 | 50 | function xopt = test_transpose_hyperbolicfactory()
n = 10;
N = 5;
transposed = 1;
if transposed % BM: okay
trnsp = @(X) X';
else
trnsp = @(X) X;
end
problem.M = hyperbolicfactory(n, N, transposed);
Y = randn(n+1, N);
problem.cost = @cost;
problem.egrad = @egrad;
problem.ehess = @ehess;
function ... |
98421ec4d914b69cbc73e05e7f40be6592dc747052b41017e9b9151ce7eacc30 | MATLAB | 716 | 32 | %% weights = sepia_utils_compute_weights_v0p8(fieldmapSD,mask)
%
% Input
% --------------
% fieldmapSD : standard deviation of fieldmap
% mask : signal mask
%
% Output
% --------------
% weights : weighting map
%
% Description: (For legacy purpose) This is how SEPIA calculate the weights
% before v1.0... |
8de82232d924bdb8f61dadbf11addbac769fab1b952c70db209111230199452a | MATLAB | 717 | 30 | function [model] = tapas_linear_model(model, pars)
%% Define the model.
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
model = struct('graph', []);
model.graph = cell(4, 1);
for i = 1:4
model.graph{i} = struct('llh', [], 'htheta', []);
end
model.graph{1}.llh = @tapas_linear_llh;
model.graph{2}.llh = @tapas_l... |
9ebf1ca0e15003ecffb943575f5ee5d6a20b0a3a1b7bf08ed3fd8b7614ed1c81 | MATLAB | 717 | 30 | classdef MaxPsi < FitnessFunction
% Fitness function for maximizing psi.
properties
Params = struct();
Spec = 'psi';
end
methods
function obj = MaxPsi(varargin)
% Constructor.
obj@FitnessFunction(varargin{:})
end
function... |
d47e7efec4e0e6700c21f7927555302ba2998616f9b3b699ca149855de0d2b7a | MATLAB | 717 | 19 | function pstruct = tapas_logrt_linear_binary_namep(pvec)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2016 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
% Lic... |
ea65a3b1880d3d716c892f0ce5a13bbdf70648c606ae66f5c065b04198be9b2c | MATLAB | 717 | 20 | function [m,dm] = meanNN(c,v, hyp, x)
% Nearest neighbor mean function. The mean function is parameterized as:
%
% m(z) = v_j, j = arg min_i d(ci,x) where d is the Euclidean distance and ci is
% the ith cluster center.
%
% The hyperparameters are:
%
% hyp = [ ]
%
% Copyrigh... |
0b6caa757b73ef5b0eb57f7d08dc013952fa1238e81604a18a11e1113c610b47 | MATLAB | 718 | 31 | function cols=colorScale(anchorCols,nCols,monitor)
% linearly interpolates between a set of given 'anchor' colours to give
% nCols and displays them if monitor is set
%__________________________________________________________________________
% Copyright (C) 2012 Medical Research Council
import rsa.*
import rsa.fig.*... |
343bb4d9a882b32a126ec2aa22717d6b0b2d82462d70f75fab2bad126481d0f1 | MATLAB | 718 | 29 | % put file detection to avoid overwrite
% put varargin for various option
function makeMovie(movie,Name,FPS,varargin)
% tic;
frc=0.75;
DIM=size(movie);
mm=min(min(min(movie,[],1),[],2));
MM=max(max(max(movie,[],1),[],2));
% switch
% case 'InvFilp'
% if varin{3}==YES
% At this stage, movie is flip in y-axis... |
6753dd0bfc74ddca05176bfea96aebc95edc693ffbc2f6df2563a86a9cbd03a9 | MATLAB | 718 | 20 | function [sha, ui8] = sero_pulseq_array2sha(array, ver)
% function [sha, ui8] = sero_pulseq_array2sha(array, ver)
%
% This funciton returns a 1x64 char array (128 bytes) that is unique for
% the numerical array. Note that it is sensitive to the precision specified,
% and that it is also perturbed by the optional versi... |
939e9b4be00782c9f8c978c56185a4c7391e4626aae628854c2a938e99c22f16 | MATLAB | 718 | 17 | function [ccg_data, sig_idx] = get_significant_ccgs(ccg_data, flag)
noise_distribution2 = [ccg_data.ccg_control(:, 1:50), ccg_data.ccg_control(:, 151:201)];
ccg_data.noise_std2 = std(noise_distribution2,0,2, 'omitnan');
ccg_data.noise_mean2 = nanmean(noise_distribution2,2);
sig_idx = (ccg_data.noise_std2>flag.sig_min... |
e2c98c56bffa653f06cc77c92ba505eb5e5361995b9f594484854fa5668b9fb9 | MATLAB | 718 | 24 | % (C) Copyright 2020 CPP visual motion localizer developpers
function varargout = preSaveSetup(varargin)
% varargout = postInitializatinSetup(varargin)
% generic function to prepare structures before saving
[thisEvent, iBlock, iTrial, duration, onset, cfg, logFile] = ...
deal(varargin{:});
t... |
9be71d3d3e99be7ef180b8ceb78a1724d4446c1c24251f8e5020b5129fe12267 | MATLAB | 719 | 24 | function [u,y,R]=Create_Dissimilar_Vectors(NumElements,avg_FR,rho,RS)
u = rand(NumElements,1);
% Force u to have mean = avg_FR (does not affect Pearson corr definition)
u = u(:);
u = u + (avg_FR - mean(u));
% Build y with corr(u,y) = rho (Pearson)
uc = u - avg_FR; % centered u (since mean(u)=avg_FR)
... |
d938f4da560e8d8445723c53af72b749cb968bd0f26b7f8a440731489205696b | MATLAB | 719 | 24 | function C=clustering_coef_bu_fast(G)
n = size(G,1);
% binary, symmetric, zero diagonal
G = G~=0;
G(1:n+1:end) = 0;
G = G | G.'; % ensure symmetry
% convert to sparse if reasonably sparse
if ~issparse(G) && nnz(G) < 0.25*n*n
G = sparse(G);
end
k ... |
116688798cacce1c3cd80da8d258f738642c1acfefde8630ab173c1a9a6a625e | MATLAB | 721 | 32 | function DI=dunns(clusters_number,distM,ind)
%%%Dunn's index for clustering compactness and separation measurement
% dunns(clusters_number,distM,ind)
% clusters_number = Number of clusters
% distM = Dissimilarity matrix
% ind = Indexes for each data point aka cluster to which each data point
% belongs
i=cl... |
6007c3087efdd694625fd5cf4b3e71e8021b957a5b94e8a4997ed52ff9f68884 | MATLAB | 721 | 27 | %% function [resnorm,residual] = ResidualGivenQSMLocalFieldDipolekernel(chi,localField,kernel)
%
% Description: compute the residual and residual norm given the local
% field, dipole kernel and QSM
%
% Input
% -----
% chi : QSM
% localField : local field perturbatios
% kernel ... |
c09b83f0b96c88334a6c49f7aaf36261f567483c807788ee68df0a9938e0a066 | MATLAB | 721 | 21 | function [mean_iti, sem_iti, p] = iti_by_reward(data)
first_trial = [1; cumsum(data.ntrials(1:end-1))+1];
data.ITI(first_trial) = nan;
data.ITI(data.ITI>prctile(data.ITI, 99)) = nan;
post_vios = logical([0; data.vios(1:end-1)]);
usethese = ~post_vios & data.block==1;
l = data.ITI(usethese... |
4ac11b7f80927b6cb31202f6057a0d6dfcc652ffc2242d97c6280f559fbb62de | MATLAB | 722 | 36 | function [ output_args ] = cell_union( input_args , mode )
%CELL_UNION( input_args , mode ) Returns the union of all sets (vectors) in
%the a cell array.
%
% INPUT:
% input_args [1x? cell]: cell array of sets (vectors)
% mode [string]: union mode ('','sorted','stable')
%
%
% === Jan Moelter, The University of Q... |
9cb3a106ac8fb7813835aedf30a752955195b917b73c6da8e5894f0cdcd9cdd0 | MATLAB | 722 | 25 | function varargout = covLINard(varargin)
% Wrapper for Linear covariance function covLin.m.
%
% Linear covariance function with Automatic Relevance Determination (ARD). The
% covariance function is parameterized as:
%
% k(x,z) = x'*inv(P)*z
%
% where the P matrix is diagonal with ARD parameters ell_1^2,...,ell_D^2, wh... |
ebc468e646cb48baaaadb2e06dd3f6ba3055af0af48ee5598273b0e24a2e2fae | MATLAB | 722 | 26 | %CheckChronux - Make sure chronux is installed and functional.
%
% USAGE
%
% CheckChronux
% Copyright (C) 2007-2014 by Michaël Zugaro
%
% 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; eithe... |
98ba73677baf38c3b580aa1ca33785b6739e00ec9172d2afaf8490e87cc0c7fa | MATLAB | 723 | 32 | function set_tick_timestamps(axes, use_milliseconds)
%% Find nice round numbers to use
number_of_ticks = 6;
x_lim = xlim(axes);
xrange = x_lim(2) - x_lim(1);
xrange = xrange / number_of_ticks;
nice = floor(log10(xrange));
frac = 1;
if nice > 1
frac = 4;
end
nice = round(xrange * frac / 10^nice) / frac * 10^nice;
... |
1da6c4384112dc1efe7acc250943fa37a6d096ebd294490c625afdbdcfef5c5a | MATLAB | 724 | 35 | function ang = pix2angle(display,pix)
%angle = pix2angle(display,pix)
%
%converts monitor pixels into degrees of visual angle.
%
%Inputs:
%display.dist (distance from screen (cm))
%display.width (width of screen (cm))
%display.resolution (number of pixels of display in horizontal direction)
%
%ang (visual ang... |
9831dbaf86d5a74328da18e10e5f46f7b6b585c2c2821005fa09c2741b16e4ef | MATLAB | 724 | 30 | classdef MinLoss < FitnessFunction
% Fitness function for minimizing loss.
properties
Params = struct();
Spec = '-loss';
end
methods
function obj = MinLoss(varargin)
% Constructor.
obj@FitnessFunction(varargin{:})
end
fun... |
a2fc61812f028fba28664c27ff5277a2cd57e0ec2fa9f458491b3def7bd4234e | MATLAB | 724 | 27 | %% function img = load_nii_img_only(filename)
%
% Description: Load images data only
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 9 October 2016
% Date modified: 11 September 2018
% Date modified: 26 June 2020 (v0.8.0)
%
function img = load_nii_img_only(filename)
% try
% info = niftiinfo(filen... |
05e9aa7ea05a8897e4d154c476c4858097eaa05156998426b24ff1673e18075b | MATLAB | 725 | 27 | function [] = image_thr(im,thr);
% this function takes an image (im) and a threshold (thr) as its input. It
% thresholds the image and displays the values *bellow* the threshold in
% red. The other values are shown in grayscale.
%__________________________________________________________________________
% Copyright (C)... |
12659f4c6080136ea0469ea3254d99a578883732ca5af5df7d21624d45e2a327 | MATLAB | 725 | 25 | function Irecord = select_recording_neurons(params)
% SELECT_RECORDING_NEURONS - Choose neurons to record
%
% H1 Line: Select random neurons for detailed recording
%
% Syntax:
% Irecord = select_recording_neurons(params)
%
% Description:
% Randomly selects excitatory and inhibitory neurons for
% recording synapti... |
1a980286524fef346bda1f1e8342d5b3e81a7bb575ccb51cb65795d0c7abfcd3 | MATLAB | 725 | 22 | function [Q, R] = orthogonalizetwice(M, x, A)
% Orthonormalizes a basis of tangent vectors twice for increased accuracy.
%
% function [orthobasis, R] = orthogonalizetwice(M, x, basis)
%
% See help for orthogonalize. This function calls that algorithm twice.
% This is useful if elements in the input basis are close to b... |
b99336003f4af84259942f2c46fa52bbb860845276d6a6e24dba0701035560d5 | MATLAB | 725 | 18 | function [this_attack_start_times,this_attack_stop_times] = filt_event_timestamps(this_attack_start_times,this_attack_stop_times,min_dur, max_isi)
% discard events that are too short and merge events close together
% merge close events
isi = this_attack_start_times(2:end) - this_attack_stop_times(1:end-1... |
3e7301cbcc281786b20f3b75677a88409b94761574eba6ba1083bdb4f3c10851 | MATLAB | 727 | 31 | %% get_set_bfr_lbv(h,mode,input)
%
% Input
% --------------
% h : structure contains all handles of SEPIA
% mode : 'set' - extract information from GUI to config file
% 'get' - extract information from config file to GUI
% input : if mode is 'set' then input should be fid
% ... |
f0dcf2618b9752e8a13c1024f80b81d39768563100208d04c81c8c408ee7ec39 | MATLAB | 727 | 42 | function [f] = zeta(z)
%ZETA Riemann Zeta function
%
%usage: f = zeta(z)
%
%tested on version 5.3.1
%
% This program calculates the Riemann Zeta function
% for the elements of Z using the Dirichlet deta function.
% Z may be complex and any size. Best accuracy for abs(z)<80.
%
% Has a pole at z=1, z... |
24405925440b02119e4d4c49bdedc4b45b8014596acbf14197d7be63fc08507c | MATLAB | 729 | 31 |
function [Ts] = Calculate_t(P,Q, polarity_list)
max_iterations = 50; % Maximum number of iterations
NS = createns(Q,'NSMethod','kdtree'); % Create Kdtree
Ts = [0,0];
j=0;
while j<max_iterations
j=j+1;
[idx,~] = knnsearch(NS,P,'k',1);% kdtree finds the nearest points to a point and returns the position of the ... |
b9a492eded4f4e7d381b915cb945b3c949d6127b5b28b7a67bfc01b410ceaac7 | MATLAB | 729 | 41 | function mfunc_ActivityMap(vectorList, LocalMinIndex, Name)
% Show activity map
[sy, sx] = size(vectorList);
if (nargin < 3) || isempty(Name)
Name = 1:sy;
end
dat = vectorList(:,LocalMinIndex);
dat = [dat, dat(:,end)];
dat = [dat; dat(end,:)];
figure(103);
h = surf(dat);
view([0 90]);
colormap([... |
4ffa6e98bfad7423f8ab3d1bfe1d1cf21a8988ea7f59a9743bcfeeb5d64e222c | MATLAB | 730 | 35 | function [llh] = tapas_sem_multiv_llh(data, theta, ptheta)
%% Compute likelihood of the eye movement model in a hierarchical format.
%
% Input
%
% data -- Stucture array of dimension Nx1 with fields y and u
% theta -- Structure array of dimension 1 X 1
% ptheta -- Priors
%
% Ouput
%
% ... |
63b77ea7d5584996b226aea9f6e9838e09b5ffd11c9d983e9d6473bfd87a0e11 | MATLAB | 730 | 29 | function r = circ_dist(x,y)
%
% r = circ_dist(alpha, beta)
% Pairwise difference x_i-y_i around the circle computed efficiently.
%
% Input:
% alpha sample of linear random variable
% beta sample of linear random variable or one single angle
%
% Output:
% r matrix with differences
%
%... |
a85e4d1a1726a123caff12cc5538ceee864a16806516d2db0872e4f079cbc55a | MATLAB | 730 | 24 | function tpl = loadtpl(tpl,handle)
%TEMPLATE/LOADTPL Read a template from file
% TPL = LOADTPL(TPL,HANDLE) read the template file associated with the
% handle HANDLE in the template TPL and store it in the variable HANDLE.
% Copyright (C) 2003 Guillaume Flandin <Guillaume@artefact.tk>
% $Revision: 1.0 $Date: 2003/... |
fe0f9b26908fa683e79c17da572a507e7c6efa60a258819da616ec716079bdce | MATLAB | 730 | 24 | %% Figure 5 S2
YOURDATAPATH = '';
savePath = [YOURDATAPATH '/' 'models' '/'];
%% Load model outputs
load(sprintf('%sall_regression,M1,angles,radrates', savePath), 'outputsM1_rr')
load(sprintf('%sall_regression,S1,angles,radrates', savePath), 'outputsS1_rr')
%% Panel A and B:
% RADICaL angles proximal/distal partial d... |
9da6251449390597478e9625bede67d0d0f4d8bf048881dce1dacaadc380e39e | MATLAB | 731 | 21 | % for each eye position, determine which circles it falls in
function circlemembership = fillcirclemembership(x, y, xrange, yrange, lut)
circlemembership = zeros(diff(yrange)+1,diff(xrange)+1) ;
for ii=1:length(x)
if ~isnan(x(ii)) && ~isnan(y(ii))
x0 = round(x(ii)-xrange(1)+1) ;
y0 = round(y(ii)-yrang... |
dad503ee623bc369fe8be3f15e9139cc6f7809cb2d7baaac3b6fea666685c536 | MATLAB | 731 | 37 | function [ptheta] = tapas_sem_prosa_later_gaussian_priors()
%% Generates standard priors for a gaussian distribution.
%
% Input
% ptheta -- Structure with the priors.
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
DIM_THETA = tapas_sem_prosa_ndims();
ptheta = struct();
[mmu, mvu, vmu, vvu, me, ve, ml, ... |
1002ffee8989304649ac48de2de4a25a99fa1b4c7a7a0edc048b6fcda634d0ae | MATLAB | 732 | 29 | %% get_set_bfr_BFRnet(h,mode,input)
%
% Input
% --------------
% h : structure contains all handles of SEPIA
% mode : 'set' - extract information from GUI to config file
% 'get' - extract information from config file to GUI
% input : if mode is 'set' then input should be fid... |
582691e790fea121143d4354a183f075ca19b8edb133eda347616530cd83661a | MATLAB | 732 | 33 | clc;
clear;
enrich_file = 'C:\Users\lihon\Desktop\abcd_study\pnc\vis_v2_r400_ro1\GOCOMPONENT.xls.xlsx';
tbl = readtable(enrich_file, 'VariableNamingRule', 'preserve');
go_term = tbl{:, 1};
go_desc = tbl{:, 2};
p_val = tbl{:, 3};
q_val = tbl{:, 4};
enrichment = tbl{:, 5};
B = tbl{:, 7};
b = tbl{:, 9};
figure; hold o... |
6b4d8c2cc7d8e03eb589e5681ff42beb7923d4a3ba03364f31491945762d21a3 | MATLAB | 732 | 30 | function img_new=cropped2full(CroppedImage,FullImage)
%Convert cropped image to full size image in MNI space
%Read in cropped image. This image will be converted to full size
[~,img_crop]=read(CroppedImage);
%Read in original full size mask.
[~,img_full]=read(FullImage);
%Dimensions of full image
N=size(i... |
97afa6dca99c5348b81572e2d61c1e7747fd5a84439b567538348cbbb7230b31 | MATLAB | 732 | 27 | function Q = qGetRotQuaternion( teta, rotationVector )
% qCreateRotQuaternion: outputs a quaternion which is used to perform
% rotation
% Q = qGetRotQuaternion( teta, rotationVector )
% IN:
% teta - rotation angle
% rotationVector - vector around which the rotation will be performed
%
% OUT:
% Q - rotatio... |
a9648aaf060654ee34b35c665fdc82fadf74025b7c69e6ecf39d00d996585fdb | MATLAB | 732 | 17 | %% Miniscope PC dropbox matlab folder
matlab_path = 'C:\Users\Zoe\Dropbox\Matlab';
%% set up fonts
set(0,'defaultAxesFontName','Arial')
set(0,'defaultfigurecolor',[1 1 1],'DefaultTextColor', [0, 0, 0])
set(0,'DefaultAxesColor',[1 1 1])
set(0,'DefaultAxesXcolor', [0, 0, 0], 'DefaultAxesYcolor', [0, 0, 0], 'Default... |
ce9f6e6242d75e357f5d3569cc8313f47e04a46db5db6d45beff7c0ede14c752 | MATLAB | 732 | 28 | function X = arg_setdirect(X,value)
% Recursively set the arg_direct flag in a data structure to the given value.
% [Result] = arg_setdirect(Data,Value)
%
if nargin < 2
error('please supply a value'); end
if isempty(X), return; end
if iscell(X)
for k=1:numel(X)
X{k} = arg_setdirect(X{k},value);
... |
0c80f32cd57979e0786a5d6ac9c22a135feffa1e53ca5be775c06582c8cf610c | MATLAB | 733 | 22 | function T = perform_tensor_recomp(e1,e2,l1,l2)
% perform_tensor_recomp - create the tensor field corresponding to the given eigendecomposition.
%
% T = perform_tensor_recomp(e1,e2,l1,l2);
%
% 'e1(i,j,:)' is the main eigenvector at location (i,j)
% with associated largest eigenvalue 'l1(i,j)'.
% 'e2(i,j,:)... |
57baf02725b17c595a0b3c45e30e5b26f72eda8711ff2527ae535b62229ec2db | MATLAB | 733 | 31 | function [ c_path_times ] = c_pathways( Pks_Frame,sec_Pk_edos )
%28Mar14 Para encontrar el numero de rutas diferentes en un experimento.
%times_secb tiene que ser un arreglo
[ d_sec,times_sec ] = d_assemblies( Pks_Frame,sec_Pk_edos );
times_secb=cell2mat(times_sec);
d_sec_time=cat(2,d_sec,times_secb);
d_st_1a=sortrows... |
1ee875204f394f1c9db19268d2a6db7cdba46d450769cf917d8f98da3440fdc2 | MATLAB | 734 | 25 | function vl_simplenn_start_parserv(net, ps)
%VL_SIMPLENN_START_PARSERV Setup a parameter server for this network
% VL_SIMPLENN_START_PARSERV(NET, PS) registers the network
% parameter derivatives with the specified ParameterServer instance
% PS and then starts the server.
for i = 1:numel(net.layers)
for j... |
9db8a5a01bc22dda2cef41be3a677a3c209077bc89fa65dce5eec9183fc8b80b | MATLAB | 734 | 25 | function unit_vector = normalise(v)
%
% Normalisation
%
% normalise(v) produces a unit vector that is in the same direction as the
% vector v. Both column vectors and row vectors can be normalised. An error
% is returned if the zero vector is attempted to be normalised.
%
% For example, normalise([1 1]) produ... |
591c8111944f4c0d2da776a8089268a55807c31165408e429aebd26c5b1e53da | MATLAB | 735 | 34 | function [llh] = tapas_dlinear_llh(data, theta, ptheta)
%% Likelihood function of a linear model where we assume that the covariance
% is diagonal. Note that this is the prior of a Gamma Gaussian model.
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
y = data.y;
u = data.u;
theta = theta.y;
[~, nc] = size(y);
l... |
1b7d228d60d901e0900cb3e4eedec8aea389c4d7b4e09972684a00bd62a12f5e | MATLAB | 736 | 25 | function getMemoryUsage()
%GETMEMORYUSAGE Summary of this function goes here
% Detailed explanation goes here
% Get memory usage
if ispc
user = memory;
total_mem_usage_mb = user.MemUsedMATLAB / (10.^6);
else
[tmp pid] = system('pgrep MATLAB');
pid_split = strsplit(pid);
total_mem_usage_mb =... |
1bed8a1ae771555ac061e71bd8d55fddf26bc74e3ccd129354db5b206b8ce885 | MATLAB | 737 | 21 | function ptvalidateparamin(x,y,arg)
%PTVALIDATEPARAMIN Validate input parameters of PERMUTOOLS functions.
% PTVALIDATEPARAMIN(X,Y,ARG) validates the input parameters X and Y, and
% input arguments ARG of the main PERMUTOOLS functions.
%
% See also PTPARSEVARARGIN.
%
% PERMUTOOLS https://github.com/mickcrosse/P... |
bc4b20d06bba531ddb62cd95150d0c203fdb6476bc17ccf123f112959650300a | MATLAB | 737 | 32 | %% get_set_qsm_lpcnn(h,mode,input)
%
% Input
% --------------
% h : structure contains all handles of SEPIA
% mode : 'set' - extract information from GUI to config file
% 'get' - extract information from config file to GUI
% input : if mode is 'set' then input should be fid
... |
f4729ccf3ed27233e1e3f7a2e23ecac860e56d975d0677ab8d1f9aa5fdb00a34 | MATLAB | 737 | 21 | function ptvalidateparamin(x,y,arg)
%PTVALIDATEPARAMIN Validate input parameters of PERMUTOOLS functions.
% PTVALIDATEPARAMIN(X,Y,ARG) validates the input parameters X and Y, and
% input arguments ARG of the main PERMUTOOLS functions.
%
% See also PTPARSEVARARGIN.
%
% PERMUTOOLS https://github.com/mickcrosse/P... |
a60de729b9a0e10679732fe8c23292465271a893c63e58c173b0cf5dea4390a1 | MATLAB | 738 | 23 | function run_peth(cluster1,cluster2,rez)
edges = -50:1:50;
Spike_id = find(rez.st(:,3)==cluster1);
M1 = rez.st(Spike_id,2);
Spike_id2 = find(rez.st(:,3)==cluster2);
M2 = rez.st(Spike_id2,2);
TrialN = length(M2);
C = zeros(TrialN,length(edges)-1);
SpikePETH_M = zeros(length(edges)-1,1);... |
eb18d2e5285354e5f0e8c528e955251ea1323dfc7f5dc829224b875483a66293 | MATLAB | 738 | 34 | function [hf,ha,figI]=selectPlot(figI)
% - activates or creates figure figI(1)
% - activates or creates plot [figI(2:4)],
% or [1 1 1] if figI(2:4) are missing
% - sets background color to white
%__________________________________________________________________________
% Copyright (C) 2009 Medical Research Council
... |
f7baa0acb9d41152a668ddab753cb896c5d4361e4452dc866a5ea33490604495 | MATLAB | 738 | 22 | function outTrain = downSampleSum(spikeTrain, newSampleNum)
%downSampleSum performs downsampling via summation (basically binning) of
%2D matrices.
% Author: Tim Sit
% Last Update: 20180518
% INPUT
% spikeTrain | numSamp x numChannel matrix
% newSampleNum | new sampling rate to use, ie. the num... |
577717bb0eb2fe975d4441fb723679aafeecbabd901bfdff37d1292305614942 | MATLAB | 739 | 26 | function A = functional2system(FC)
% Translate functional connectivities to system matrix
% A = -L/(\lambda_{max}(L))
% L is the laplacian matrix for FC
% Inputs: FC, N-by-N or N-by-N-by-M matrix, functional matrix
%
% Output: A, N-by-N, system matrix
[row,~,num] = size(FC);
if num =... |
72588fcc14e8c74b0672d68d4f1326f08f9b443047f8b39c526f56453f824d33 | MATLAB | 741 | 37 | function h = plot_maps(fit)
% h = plot_maps(fit)
% Plot parameter maps from model
%
% USAGE:
% h = plot_maps(fit)
%
% INPUTS:
% fit = fit results from IVIM model
%
% OUTPUTS:
% h = figure handle
%
% AUTHOR:
% Dr. Helge Zoellner (Johns Hopkins University, 2025-06-12)
% ... |
06ddcf0edc5bf525bfd4807b34753d1763b9b41eef39b90509ae5973afcb8ba4 | MATLAB | 742 | 28 | function [handle,matrix,u] = semplotBin(x,y,nBins,varargin)
if size(y,1)==1, y = y'; end
if size(y,2)>1, y = y(:); end
if size(x,1)==1, x = x'; end
if size(x,2)>1, x = x(:); end
if numel(x) ~= numel(y), error('x and y should be vectors of equal length'); end
nans = isnan(x);
x(nans) = []; y(nans) = [];
if nBins==0
... |
3214338f410205f2fbab62a6591b06af1a11e953609333c10d102dff367dc6e1 | MATLAB | 742 | 37 | function RHSdiv = divergenceTerm1D(F)
% This function calculates the divergence of a field using its face
% average value
%
% SYNOPSIS:
% RHSdiv = divergenceTerm1D(F)
%
% PARAMETERS:
% F: Face Variable
%
% RETURNS:
%
%
% EXAMPLE:
%
% SEE ALSO:
%
% Copyright (c) 2012-2016 Ali Akbar Eftekhari
% See the license file
... |
6396d6ad9b8b9e69c6b5a3c9dc6e2a6552c8173ed718760d47faf6f1cc168a0a | MATLAB | 742 | 28 | function err = TCA_chooseRank(data, savePath)
% plots the error for a variety of different rank models, used to select
% rank for the model
%% Fit CP Tensor Decomposition
% these commands require that you download Sandia Labs' tensor toolbox:
% https://github.com/andrewssobral/tensor_toolbox/
% https://www.tensortool... |
fa1d5990ea1829bdf3aafdfa10faedcbae4e49bcc2ae450a908d88b912b2f4f5 | MATLAB | 742 | 33 | function RHS = constantSourceTerm2D(phi)
% RHS vector for a Explicit source term
%
% SYNOPSIS:
% RHS = constantSourceTerm2D(phi)
%
% PARAMETERS:
% phi: Cell Variable
%
% RETURNS:
% RHS: vector
%
% EXAMPLE:
%
% SEE ALSO:
%
% Copyright (c) 2012-2016 Ali Akbar Eftekhari
% See the license file
% extract data from t... |
c57e3bfd46315c8121ee6390ee9b3d63eee9b20e67ef6c0b546865931f079a1d | MATLAB | 743 | 30 | clear
numCams = 6;
baseFolder = 'D:\\20191122\mouse';
load([baseFolder filesep 'calibration\camera_params.mat'])
load([baseFolder filesep 'calibration\intrinsic\cam_intrinsics.mat'])
% extrinsics
% r = rotation matrix
% t = translation matrix
% intrinsics
% K = intrinsic matrix
% RDistort = RadialDistortion
% TDisto... |
bc9fa35dd74958557c244151781c4b5e591f3dfbedaa13ae22974b0235639979 | MATLAB | 744 | 24 | function X = hlp_applyscaling(X, si)
% Apply some previously determined scaling structure
% X = hlp_applyscaling(X, ScaleInfo)
%
% This is just a convenience tool to implement simple data (e.g. feature) scaling operations.
%
% Examples:
% scaleinfo = hlp_findscaling(data,'whiten')
% hlp_applyscaling(data,scaleinfo... |
dc599960f4c0a71e1fbbf7b75465b32d50c5825ffd22780305ec262f8128217a | MATLAB | 744 | 44 | function x0 = sero_srr_setGuess(S, TR, B, W, do_t1, do_v, sm_siz)
% function x0 = srp_setGuess(S, TR, B, W, do_t1, sm_siz)
z = size(TR,2);
TRnan = TR;
TRnan(TRnan==0) = nan;
if nargin < 4 || isempty(W)
W = TR>0;
end
if nargin < 5 || isempty(do_t1)
do_t1 = 1;
end
if nargin < 6 || isempty(do_v)
do_v = 1;
... |
e35038cbd9d6350ececb190c364c602e3211cf43732cf89a014b16c3f27388a0 | MATLAB | 744 | 29 | classdef nnrelu < nntest
properties
x
end
methods (TestClassSetup)
function data(test,device)
% make sure that all elements in x are different. in this way,
% we can compute numerical derivatives reliably by adding a delta < .5.
x = test.randn(15,14,3,2) ;
x(:) = randperm(numel(x)... |
33d46c5b14e337c73375f5a77d762316e2f9fc4fb14db785e7f2f76b9145aaa7 | MATLAB | 745 | 24 | function mad = compute_MAD(inputVector)
%It computation is based on the
%following article: https://www.sciencedirect.com/science/article/pii/S0022103113000668
%This indice is to be better than the standard deviation because it is
%less sensible to outlier. The script assume that the data approximatively normaly distri... |
45c4c3abf62535b59a26685c56c24b386d43fd8e7139469924dbd9d176599bc5 | MATLAB | 745 | 28 | function [eyelikeres, S, P]= eyelike(E)
% EYELIKE - calculate a permutation matrix P and a scaling (diagonal) maxtrix S
% such that S*P*E is eyelike (so permutation acts on the rows of E).
% E must be a square matrix.
% Usage:
% >> [eyelike, S, P] = eyelike(E);
%
% Author: Benjamin Blanke... |
92d204223a08c78757006b58a098434ef2b7476ba23781b8dafd37bb6f7a109d | MATLAB | 745 | 16 | function [seq_ent,seq_maxent,dkl] = compute_HOM_seq_ent(nsymbs,symbprobs)
% Computes the entropy for a k-th order markov chain sequence
% seq is a sequence of integers (symbols) going from 0 to max(seq)
%
%nsymbs = length(symbprobs);
%minprob = eps;
%symbprobs(symbprobs==0) = minprob;
symbprobs=symbprobs(symbprobs>0);
... |
be2b4beafb47f43fcf039d4410ab1d99013e640c46e2956e66532acb8c3ef313 | MATLAB | 745 | 39 | function pix = angle2pix(display,ang)
%pix = angle2pix(display,ang)
%
%converts visual angles in degrees to pixels.
%
%Inputs:
%display.dist (distance from screen (cm))
%display.width (width of screen (cm))
%display.resolution (number of pixels of display in horizontal direction)
%
%ang (visual angle)
%
%Wa... |
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