sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
36d256e7471fe18e3955feae2cc538578c460f261d5012829c42d459756e6717 | MATLAB | 1,195 | 42 | function freezeColors(varargin)
%FREEZECOLORS Freeze current colormap to prevent changes
%
% Purpose:
% Locks the current colormap so that subsequent colormap changes don't
% affect the current figure or axes.
%
% Usage:
% freezeColors() % Freeze current axes
% freezeColors(h) % Freeze specific... |
8a086bcef6f232a67893b7ec57d2d7f50f55208820c1301abe6d3c74109f9ee7 | MATLAB | 1,196 | 34 | function getTriggers_switchEI_stimuliCondition(params)
% determines trials which contained the selected keyword (in params.thisCategory)
% MUST match trials 'tr' with the same keyword in trials(tr).stim_cond
% saves result into respective column of 'trials_events' in each sessionCacheFile
% - rows = trials
% - valu... |
dd00a56e9bb7d1c8644425e047fd56980d35e4188c5ac1cfc04454f4cc3fa748 | MATLAB | 1,198 | 29 | function [lp,dlp] = priorTransform(g,dg,ig,prior,x)
% Transformed univariate hyperparameter prior distribution.
% Compute log-likelihood and its derivative or draw a random sample.
% The prior distribution is parameterized as:
%
% prior(y), where y = g(x),
%
% g is the transformation function (monotonically increasin... |
23205e3effb3d331c5a4093ac65b9fe9b1d0d98b020a72801006890dc8fa31c1 | MATLAB | 1,199 | 36 | function test_suite = test_getDesignInput %#ok<*STOUT>
% (C) Copyright 2021 CPP visual motion localizer developers
try % assignment of 'localfunctions' is necessary in Matlab >= 2016
test_functions = localfunctions(); %#ok<*NASGU>
catch % no problem; early Matlab versions can use initTestSuite fine
... |
272679e52f84f63ece9bd7ef7e49d70fdbe3b0a30f1ff2fcd9edd39f9887782c | MATLAB | 1,199 | 22 | function fieldmap = compute_fieldmap_analytical(theta, phi, sus_my, label_mask, r, r_o, r_i)
% Calculate fieldmap using the analytical solution, derived from Xu thesis
masksize = size(label_mask);
fieldmap = zeros(masksize);
% iterate over indices
for i = 1:masksize(1)
for j = 1:masksize(2)
if label_mask(i,... |
637121fc78b0026223c7416ef0b5ccdd708a4d8ff28837d4e186c6808a934bbb | MATLAB | 1,199 | 33 | % logging_fcallstack_format() -
% Usage:
% >> logging_fcallstack_format(formatstr)
%
% Inputs:
% formatstr - Set the formatting for logging_fcallstack
% sets CALL_STACK_FORMAT
% matlog - a Matlab and Octave compatible logging library
% Copyright (C) 2017 Mae Kennedy
%
% This program is free softw... |
e8431916d38203d4778640a768f2d95d1a75d50f3c52e406d4fbc835d87dd8a9 | MATLAB | 1,199 | 45 | function Y = tapas_uniqc_create_shepp_logan_4d()
% Creates 4D Shepp-Logan Phantom for tapas_uniqc_slider4d demo
%
% output = tapas_uniqc_create_shepp_logan_4d(input)
%
% IN
%
% OUT
%
% EXAMPLE
% tapas_uniqc_create_shepp_logan_4d
%
% See also
% Author: Saskia Bollmann & Lars Kasper
% Created: 2015-11-20
% Copy... |
d65929fb15a80c20797f8b941b6caecf5f1743b8b7491954f84b731ba119b348 | MATLAB | 1,200 | 65 | function custom_colormap=getCurrentColormap(varargin)
% EXAMPLE USE WITH ARGUMENTS
% getCurrentColormap() - use 1
% getCurrentColormap(name) - use 2, etc.
% getCurrentColormap(name,options) - use 2, etc.
%
% HELP
% Getting custom colormap and exporting it.
%
% HISTORY
% - 20-05-09 16:13:59 - created by Radek Chrapkiewi... |
e01cdda0fc15ec347a2430c13ae7d6046d099dabfc513533bdd2c65b4d5a5871 | MATLAB | 1,200 | 43 | function mov = getImageData(params, fn, filesForROI, averageFiles)
if averageFiles
mov = getAvgMov(fn, params.Nplanes, filesForROI(1:averageFiles));
mov = mov(:,:,params.framesToDisregard:end);
else
mov = getMov(fn, params.Nplanes, filesForROI, params.framesToDisregard);
end
function im = g... |
ff317fd1ce96813e7b4f9650f31b0819b10b7157478b0a328a9b2f664f21d881 | MATLAB | 1,200 | 43 | function PlotExtendedData8(datadir, codedir)
%PlotExtendedData8 - Plots Extended Data 4.
% INPUTS:
% datadir - Local directory where ProcessData_ExtendedData8.mat was saved after running ProcessData_ExtendedData8
% codedir - Local directory where code (e.g., published/EstrousRPE/) was saved
%% Set up paths
s = pa... |
467b04a0298de5467006e2ff3169975a0ddc3a5e85c2d6872e930372182c0e13 | MATLAB | 1,201 | 30 | %{
tuning.DotRFMap (computed) # receptive field from the dot stimulus
-> tuning.DotRF
-> preprocess.SpikesRateTrace
-----
response_map : blob # average response for each location
center_x : float # (fraction of x) center of receptive field on x, from Gaussian fits
center_y : ... |
d38be5a0f2206fb2423a5d75a90e9b2c8728a0b520f40a9b9ddcb502ec1e4ff1 | MATLAB | 1,201 | 39 | function nullStats = GiveMeSimpleNullStats(groupLabels,numNulls,cfnParams,meanOverFolds)
% Returns simple permutation-based null samples
%-------------------------------------------------------------------------------
% Check inputs and set defaults:
if nargin < 4
meanOverFolds = true;
end
%----------------------... |
2207c1fea1acb02ac8b7b3ff7f22755da244b745985245ebf50e5675da999dd1 | MATLAB | 1,202 | 42 | function [o1,ovec1,ovec2,xyzo] = overlap(cla1,cla2,varargin)
% function [o1,ovec1,ovec2,xyzo] = overlap(cla1,cla2,[v1,v2])
%
% tor wager
% o1 and o2 are overall measures of overlap
% ovec1 and 2 are for each cluster
% cla1 and 2 are the clusters structures
% v1 and v2 are optional vectors indicating cluster memberships... |
23a9e7241eecd58741673d5669ee16b5b6b7ac8d7e5b5934a8bab851695e86cf | MATLAB | 1,202 | 34 | function result = hlp_iscaller(func, level)
% Test whether some function is calling this function at some level(s) of indirection.
% Result = hlp_iscaller(Function, Levels)
%
% It can be specified what levels of nesting outside the function which runs hlp_iscaller are considered.
%
% In:
% Function : function handle ... |
44c2fa390aaabe8beb940321905c83eb34fb1c16aee267c46a57bce2f6425f84 | MATLAB | 1,202 | 39 | function [XYZr] = RotateAboutAxis(XYZ, nrm, phi)
%[XYZr] = RotateAboutAxis(XYZ, nrm, phi)
%yet another function to perform rotations about an axis
%XYZ: Matrix of XYZ coordinates, each row is an XYZ triplet
%nrm: axis of rotation
%phi: Clockwise rotation angle in radians
%XYZr: Rotated version of XYZ
%Note:
%Origin of ... |
7e9af53558a7092b2e4a6cc3cbff6a95119dde292d0861284eb69240c9341229 | MATLAB | 1,202 | 18 | function cifti_write_sdseries(data, filename, varargin)
%function cifti_write_sdseries(data, filename, ...)
% Write a new sdseries cifti file from a 2D data matrix.
%
% The cifti extension on the filename should always be '.sdseries.nii'.
%
% To control the contents of the scalar and serie... |
0068c6459af49e524101eaa4757773d802c7e607fcb852aa6d2850016c32e5c8 | MATLAB | 1,203 | 29 | function [values] = ave_control(A)
% FUNCTION:
% Returns values of AVERAGE CONTROLLABILITY for each node in a
% network, given the adjacency matrix for that network. Average
% controllability measures the ease by which input at that node can
% steer the system into many easily-reachable ... |
f0f76f8c0d29bb616f8be757152bf2f94bcc302bd7eba9f89e834c0cbd427f05 | MATLAB | 1,203 | 53 | % op_freqshift.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_freqshift(in,f);
%
% DESCRIPTION:
% Apply a frequency shift to the input spectrum by 'f' Hz.
%
% INPUTS:
% in = input data in matlab structure format.
% f = frequency shift to apply (in Hz).
%
% OUTPUTS:
% out = Output following f... |
707b1054f19576536c49290911e9472e4add06ec0c31891e9cd41c2d7d7b43a7 | MATLAB | 1,204 | 37 | function y = binompdf(x,n,p)
% BINOPDF Binomial probability density function.
% Y = BINOPDF(X,N,P) returns the binomial probability density
% function with parameters N and P at the values in X.
% Note that the density function is zero unless X is an integer.
%
% The size of Y is the common size of the input a... |
747ebe4bd9e9b7c47a051516a80f2e19fd9e236227009133b966e48229e8487e | MATLAB | 1,204 | 40 | function [n_selective,p_selective] = selectiveNeuronCalc(A,mask1,mask2)
%SELECTIVENEURONCALC: decides via t test which neurons are selective
%for two different cases
%A: main data structure
%mask1/2: anonymous function handle that takes A and a neuron number to
%compute boolean of trials to consider for cases 1 and 2
%... |
a1d149777878cf46ef56af7e53b2791d0c19a12951e2ec681e7408d8644a34ad | MATLAB | 1,204 | 36 | %_________________________________________________________________________________
% Equilibrium Optimizer source code (Developed in MATLAB R2015a)
%
% programming: Afshin Faramarzi & Seyedali Mirjalili
%
% e-Mail: afaramar@hawk.iit.edu, afshin.faramarzi@gmail.com
%
% paper:
% A. Faramarzi, M. Heidarinejad... |
fc4f324116cfce2915a97a244957bc9941d8da0089e1daddcc561569c5cbd593 | MATLAB | 1,204 | 57 | function save_avw_img(img,fname,vtype,endian);
% SAVE_AVW_IMG(img,fname,vtype,endian)
%
% Save an array (img) as an analyse file (only the .img)
% for either a 2D or 3D or 4D array (automatically determined)
%
% vtype is a single character string: 'b' (unsigned) byte, 's' short,
% ... |
0587199b73fd8bd45d0a15cb6defbcac68f2b8cd379089b5672de21f440a3a1c | MATLAB | 1,205 | 32 | function parentNode = traverseFolderAndStop(parentNode, currentFolder)
% This only goes one folder (does not recurvesily go through folder)
% Get all contents of the current folder
contents = dir(currentFolder);
% Filter out '.' and '..' directories
contents = contents(~ismember({contents.name... |
c299257fd89029651a4ef13c8b4829d555811cd1d87b498d89105d257d34eaea | MATLAB | 1,205 | 39 | classdef Pooling < dagnn.Filter
properties
method = 'max'
poolSize = [1 1]
opts = {'cuDNN'}
end
methods
function outputs = forward(self, inputs, params)
outputs{1} = vl_nnpool(inputs{1}, self.poolSize, ...
'pad', self.pad, ...
'strid... |
c9a9acc838c08af1eb5cd1353b985df5805c05bc24c01ebc178fd924f0d0ae3c | MATLAB | 1,205 | 38 | function ss_tcs_stat = single_subject_tcs_features(ss_tcs_data)
%UNTITLED5 Summary of this function goes here
% Detailed explanation goes here
ss_tcs_stat=zeros(1, 12);
var_all=zeros(1,8);
% old version of arima estimate, excluded because of extra toolbox needed
% (econometric)
% for j_order=1:8
% mdl=arima(j_or... |
d958a17e823c3f069b7c9471cd0d5f651820f830db9351e653e849cee481d3f6 | MATLAB | 1,205 | 33 | %GlobalSettings - Initialize settings for FMAToolbox.
%
% The global variable SETTINGS holds a number of basic settings such as the
% minimum and maximum distance allowed between LEDs. Modify this variable to
% customize individual values. For instance, to change the maximum distance
% between LEDs, add the following t... |
ddb00499d7cb021957515b877eb5136ddea3f71dc86b83ec2572b4c12b067770 | MATLAB | 1,206 | 36 | % Written by Dr. Gregory Scott from Imperial College London,
% Academic Clinical Lecturer, The Computational, Cognitive and Clinical
% Neuroimaging Laboratory (C3NL) Faculty of Medicine,
% Department of Medicine, https://www.imperial.ac.uk/people/gregory.scott99
%
% 1D BDM implementation of method as described in:
% A ... |
409c8dfacde78867b1a3ec7f4a974c93fb070eff55f6a195ef18ed58bc34c6d6 | MATLAB | 1,207 | 59 | %Encuentra los elementos con mayor y menor distancia. LC
%Con ello se preserva la estructura en la proyección de LLE.
%Busca los elementos F y G que tengan la mayor distancia
%Despues busca el elemento mas cercano a F
function [DE,Delta,T_Prop,Deltab,T_Propb]=Distancia(Dist,Y)
%Elementos del triangulo, delta y propo... |
7c0a2b63fc36b6ce864e636a3716e8d9859b6ae61cf35341023e6561ed992984 | MATLAB | 1,207 | 55 | function [umxSignal]=runFastICAnd(input)
options.savePath=[];
options.figName= '_runFastICA';
options.plotFigure=true;
% Make sure M is a row matrix
if iscolumn(input)
M=double(input');
else
M=double(input);
end
% run fastICA
[icasig, ~, ~] = fastica(M','g','tanh','epsilon',1e-7,...
'stabilization','on',... |
da13f5e87bcc42c2660a9d5b2fb0ad4652c17f4e4bf2a0a9803b40c6702442e1 | MATLAB | 1,207 | 61 | function [sigma,mu,A]=mygaussfit(x,y,h,optionStab)
%
% [sigma,mu,A]=mygaussfit(x,y)
% [sigma,mu,A]=mygaussfit(x,y,h)
%
% this function is doing fit to the function
% y=A * exp( -(x-mu)^2 / (2*sigma^2) )
%
% the fitting is been done by a polyfit
% the lan of the data.
%
% h is the threshold which is the fra... |
8e761363e4c372947f52eebb4ba593f01f14f19ba622d3690ff36cc80200daa0 | MATLAB | 1,208 | 39 | classdef Pooling < dagnn_bc.Filter
properties
method = 'max'
poolSize = [1 1]
opts = {'cuDNN'}
end
methods
function outputs = forward(self, inputs, params)
outputs{1} = vl_nnpool(inputs{1}, self.poolSize, ...
'pad', self.pad, ...
'st... |
df138346c7eeb053ab270434f2b3b5268f4af453282cbf4955c166ff569f5550 | MATLAB | 1,208 | 53 | function indicesOut = randomPermutation(n)
% generates a random vector of n integer numbers from 1 to n. The numbers
% are randomly placed in the vector.
% Cai Wingfield 2-2010
%__________________________________________________________________________
% Copyright (C) 2010 Medical Research Council
import rsa.*
import ... |
4f0044ee9e5abaa6b1def0be46f612616b27a79984593715c561eaf478d46243 | MATLAB | 1,209 | 42 | % Generate Model WTs by drawing from gamma or logn distribution
function wt_mdl = generate_wts(wt_opt, nsims, noise_arg, params)
if strcmpi(noise_arg, 'gamma')
Sigma = params(1);
k = wt_opt.^2./Sigma;
theta = Sigma./wt_opt;
wt_mdl = mean(cell2mat(arrayfun(@(x) gamrnd(k, theta), 1:nsims,...
... |
52ee27d82d766c68b0ea4f09c63bb0fab650c357ca5918e3b707683000fae18e | MATLAB | 1,209 | 85 | 2
37
4
GD
2
male
female
CN
2
C1
C2
EM
3
P
U
N
SJ
10
S1
S2
S3
S4
S5
S6
S7
S8
S9
S10
1
0
20
6
../Lukas_Coarse2/m.AlvaranP051303.full.reg+tlrc.BRIK
1
../Lukas_Coarse2/m.AstorA072903.full.reg+tlrc.BRIK
1
../Lukas_Coarse2/m.BlumenkronF070103.full.reg+tlrc.BRIK
1
../Lukas_Coarse2/m.CabrerraD121002.full.reg+tlrc.BRIK
1
../Luk... |
9b9d8a3170438fe51b2f5aaa111d4b36cdbd1794685cffeb88a4cd50317bb87a | MATLAB | 1,209 | 33 | function [stl_file]=Export_STL(data_file, START_TIME, END_TIME, map, column)
% STL to Blender:
%
% This script will load LFP data from SpikeGLX bin file and export it as stl file for manual annotation
% Next, blender CSV output file is loaded back into matlab
%
% input:
% data_file: full path to ap.bin fil... |
a20dfeea4d031cfc8bf495b55b0696e00b6495ed1e1ece6038f56c3e58fafc47 | MATLAB | 1,209 | 56 | function [inference] = tapas_sem_multiv_prepare_inference(data, model, ...
inference)
%%
%
% Input
%
% Output
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
% Number of chains
nc = size(model.graph{2}.htheta.T, 1);
% Number of subjects
ns = numel(data);
% Number of real parameter and input para... |
cf46a46692b470f3d52b234745d92b47c3db3e5ec465c13f998639e595eee19b | MATLAB | 1,209 | 33 | function [spatial] = Setup_Storage(step_cap,C1,C2,C3,myelin)
% Cell 1
spatial.C1x = cell([1 step_cap + 1]); % cell array for C1 x pos
spatial.C1y = cell([1 step_cap + 1]); % cell array for C1 y pos
spatial.C1x{1} = C1.x; spatial.C1y{1} = C1.y; % initialise C1 x,y pos
% Cell 2
spatial.C2x = cell([1 step_cap... |
fc0d6af0871181cee4c17920c24d47252f67b51f4c19a7fa770722d1e8e63fa4 | MATLAB | 1,209 | 43 | function this = MrDataNd_value_operation(this, testVariantValueOperation)
% Unit test for MrDataNd for arithmetic operations (perform binary
% operation)
%
% Y = MrUnitTest()
% run(Y, 'MrDataNd_value_operation')
%
% This is a method of class MrUnitTest.
%
% IN
%
% OUT
%
% EXAMPLE
% MrDataNd_value_operation
%
% ... |
0afaa3ebaa4c7d3f1c0007ff2f2a7d015571d3d8a30e87384c45a8dc3da2bc64 | MATLAB | 1,210 | 36 | function proj_auc_gp = cal_proj_auc_random_gp_dist2sides(env1_data, env2_data, num_permutation)
% envX_data: features X cells/voxels, gird and place cells together
% num_cells should be even
n_features = length(env1_data(:, 1));
num_cells = length(env1_data(1, :));
% env1
env1_data = env1_data - repmat(mean(env1_dat... |
be700173abf44e910bf9c09d9380964ca64b5f42b8d92e9393da64a3b0ac1cc2 | MATLAB | 1,210 | 36 | function res = DK_timerev(x,timeLag)
% DK_timerev Time reversal asymmetry statistic
%
% Calculates a time reversal asymmetry statistic
% x -- the time series
% timeLag -- a time scale (in samples) default 1
%
% ------------------------------------------------------------------------------
% Copyright (C) 1996, D. Kapla... |
27fa184647ed580acc2c9b80765e59fa0aa8dafbd3cde7c03f9a88efd89cda70 | MATLAB | 1,211 | 37 | function [shuffleTauDiff, observedTauDiff, pval] =...
myTauShuffleTest(first_q, last_q, myBetas, Nshuffle)
Betas = myBetas(first_q | last_q,:);
nrats = size(Betas, 1);
shuffleTau = nan(Nshuffle, 2);
for ii = 1:Nshuffle
fprintf('shuffle %d out of %d\n', ii, Nshuffle)
shuffleLatency = randperm(nrats)';
... |
6650f1d3bfb7d08fe8a404e9efa0473986f0fdfda16750de32511680c30836fb | MATLAB | 1,211 | 37 | function getTriggers_emoReco_imageSound(params)
% finds which stimuli inlcuded Image or Sound
% concordancy paradigm stimuli:
% Image + Image
% Image + Sound (!!! sound is always "second" stimuli in trials structure !!!)
% (c) Jiri, Nov16
display([' - finding events for: ' params.thisCategory]);
%% per session: ... |
c51d84fce9862c3abc0227caf81a207a6f368ff11abca286eb3b31b6c167965f | MATLAB | 1,211 | 24 | function delta = delta_from_dist_mat(dist, rho)
% computed delta for the rho vs delta plot.
% based on clustering by density peaks
% Reference paper: Herzog et al. 2020 "Scalable and accurate automated method
% for neuronal ensemble detection in spiking neural networks"
% https://www.biorxiv.org/content/10.1101/2020.... |
ece7cc1251bfc76b4bc89a7a089fae084efa1b8327d513d529fe6be9d496f45c | MATLAB | 1,211 | 38 | function [a,b,c] = runlme(behavior , eigenvalue, toi)
eigenvalue = permute(eigenvalue,[1 3 2 4]);
for com = 1:2
for e = 1:2
for t = 1:size(eigenvalue, 4)
C = squeeze(eigenvalue(:, com, e, t));
behavior.C = C;
formula = 'C ... |
f1affd8efb9a46281514e95c1786b9f2c7e5dcb27e596c9c649a3db8541564a2 | MATLAB | 1,213 | 42 | function [dim] = pos2dim3d(pos,dimold)
% POS2DIM3D reconstructs the volumetric dimensions from an ordered list of
% positions. optionally, the original dim can be provided, and the (2:end)
% elements are appended to the output.
%
% Use as
% [dim] = pos2dim3d(pos, dimold)
% where pos is an ordered list of positions ... |
636d3554658fd81cefb4e007952333ac80f35a9e4acf7f1558d0a4ee70c5aba6 | MATLAB | 1,214 | 38 | function VersionStruct = getCurrentVersion()
%% VersionStruct = getCurrentVersion()
% This function reads the current version and release date from the
% version.json file in the settings folder
%
% USAGE:
% VersionStruct = getCurrentVersion()
%
% INPUTS: none
%
%
% OUTPUTS:
% VersionStruct... |
cffdebba5c9b086764f1007e4865f39db688cda58533b58e8c40bdce06c0e917 | MATLAB | 1,214 | 38 | function exportCurrentFigAsPDF(filespec,userOptions)
% exports the current figures to the file [filespec,'.pdf'] in pdf
% format.
% filespec is the full path (including the file name) of the file to be
% saved.
% userOptions can be used to modify the dots per inch (dpi) or the
% tightness of the figure in the printed ... |
dee9b18a7618e230ac042ebd288fcad654d9ca885f4a75050f4960b9ae5bd850 | MATLAB | 1,214 | 67 |
%
% function to rotate a 3d object to a new orientation defined
% by an eigenvalue problem.
%
% inputs are either:
% X, Y, Z matrices defining points to rotate
% n x 3 pointlist of [X Y Z] values, with 2nd and 3rd args empty
%
% returns: structure with X Y Z rotated, and XYZ rotated pointlist
%
% results = rotat... |
8e35ad12e63c4f621e1db0a07c9d9aef922aa3c5084277f5e7096390091a9945 | MATLAB | 1,215 | 39 | function [Mdl] = run_lda(params)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% run_lda returns Mdl structure including function handles of fit,
% predict and score functions for linear discriminant analysis.
%
% Arguments:
% params: Structure including following hyperparameters:
% ... |
ababd74d60cbdbda62a4985c44b2dabf70c58583ed84c0e339ffa48189f24f4e | MATLAB | 1,215 | 36 | function [LP_Signal_fix, HP_Signal_fix]=filter_signal(Fs, num_electrode, Signal)
%Filtering MEA signals
% INPUTS:
% Fs - Sampling frequency (Hz)
% num_electrode - Number of electrodes (channels)
% Signal - Raw signal matrix [time x electrodes]
%
% OUTPUTS:
% LP_Signal_fix... |
be6658734a1b6555b43e03faf04fef299ef5acbd14bcc7be9e06a84b19cf3d16 | MATLAB | 1,215 | 41 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Requires: https://github.com/guorongwu/DynamicBC/
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear; clc;
%% --- Parameters ---
ts_file = 'time_series.txt'; % input time series
mu = 100; % regularisation parameter
tmp_file = '/h... |
cc776fc1f6d5b1f5ea942d7e09503c48981c677fb5784e42f9c5b38860df9170 | MATLAB | 1,215 | 34 | % Add Manopt to the path to make all manopt components available.
% This file is part of Manopt: www.manopt.org.
% Original author: Nicolas Boumal, Jan. 3, 2013.
% Contributors:
% Change log:
% Aug. 7, 2013 (NB): Changed to work without the import command
% (new structure of the toolbox).
% ... |
f362190fb42f72740630b86666dabf1303cd276208abf380da7cd74e01a8eef1 | MATLAB | 1,216 | 39 | function useCh_GW = ch2roi_assignGW(gm_wm_selection, H_channel, gm_thr)
% was channel assigned to: GREY matter or WHITE matter or CSF or BONE ?
% uses channel structure H_channel to find if
% (1) it matches the gm_wm_selection
% (2) the probablity is below threshold gm_thr
% input:
% H_channel = channel structur... |
14c4ccb992ed85ecdeab573dd85cb6286bb76ba30d37f68172c5cafc26d64526 | MATLAB | 1,217 | 54 | function Xcov = embed_cor_cov(X,D,tau,ix_act)
% Partial covariance matrix in time delay embedding space
% XX = embed_cor_cov(X,D,tau,ix_act)
% XX = X(ix_act,:)*X'
% --- Input
% X : input signal : [Xdim x Tsample x Ntrial]
% D : time embedding dimension (integer)
% tau : delay time in sample number (integer... |
2b2efc182605cdecfa5d83739a9d38bf942d9798daa4108c55c25825101ecc91 | MATLAB | 1,219 | 40 | function y = tapas_condhalluc_obs_sim(r, infStates, p)
% Simulates responses according to the condhalluc_obs model
%
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2016 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which... |
694f2f2561a3322d7cf5137d41cfafc8c49e6ddbdfb37c79a07e21aba7eba29d | MATLAB | 1,220 | 40 | function numVax = freadVAXG(fid, number, method)
% FREADVAXG Converts a number read in IEEE-LE format to its VAXG
% floating point representation.
%
% Usage:
% fid = fopen('file.vaxg', 'r', 'ieee-le');
% num = freadVAXG(fid, numElements, 'format')
%
% 'format' options are the same as FREAD.
%
% The fun... |
0cac68744b7d2260f6bb3b9333277665cf0770c7f91cae576b33de2ab1a736d9 | MATLAB | 1,221 | 34 | function zspec = cal_Z(npools, B1, concentrate, offset, T1, T2, K1, K2,M0, Exchangerate, Exchangerate_verse, w_x, T2sArr, freqArr, lineshape)
zspec = [0];
% parfor ii = 1:numel(st)
for j = 1:numel(B1)
B = B1(j);
[omega_1, ~, ~, step_size] = get_RF_pulse(B, 512);
w11 = omega_1;
% ... |
d17c5910ef2654c03fbc2137495ffd714377068d7a6fbde20b2cb979ed81ade0 | MATLAB | 1,222 | 42 | %% paths = get_sepia_toolbox_home_paths()
%
% Output
% --------------
% paths : structure with the *_HOME directories declared in
% SpecifyToolboxesDirectory.m (empty if a given toolbox is
% not configured there)
%
% Description: Small helper to read the external toolbox directories
% ... |
f4b4d573b7c0a469b035802652741093f59d6267be9a1a6b4bb1f23ee0eee5ef | MATLAB | 1,222 | 46 | function G = grammatrix(M, x, vectors)
% Computes the Gram matrix of tangent vectors in the Manopt framework.
%
% function G = grammatrix(M, x, vectors)
%
% M is a Manopt manifold structure obtained from a factory.
% x is a point on the manifold M.
% vectors is a cell containing n tangent vectors at x.
%
% G is an n-by... |
4852a7c73cea928aca60bde75086bb563b949374c9721004bff71d65306ea7de | MATLAB | 1,223 | 33 | % logging_set_log_level() - sets the logging level of logging_log messages
% to the provided level, if the level doesn't exist
% the behaviour is undefined
%
% Usage:
% >> logging_set_log_level(strlevel)
%
% Inputs:
% strlevel - maximum level to log char type
% m... |
5ab6ddea39707b2de028ae817994b2345d77521d20dac99b1ae00310de923649 | MATLAB | 1,223 | 37 | %% This script is an example of how to implement the functions for estimating curvature and their derivatives
%Author: Itzik Ben Shabat
%Last Update: July 2014
%%
%Clear all variables, close all windows and clear command window
clear all
close all
clc
%% Generate the example triangle mesh example
StepSize=... |
aea06004810bc97b3905cb91ea8f0478b0a538a2e0f722c0187bc35c0c601948 | MATLAB | 1,223 | 32 | function run_tier2()
%% run_tier2()
%
% Description: runs the Tier-2 toolbox-dependent regression matrix
% (test/tier2_matrix/) against a small, deterministically-generated
% synthetic phantom (test/phantom/generate_synthetic_phantom.m) - unlike
% Tier 3, no real dataset is required. Rows requiring an unavailable
% too... |
8f8fc11fecb60ebc7d87dc5eaf25f33ec75ef016c75ade684ab9b7f6b90e28e2 | MATLAB | 1,224 | 42 | function [out,str] = anova2_repmeas_autodesign(data,factNames,printOutFlag)
% function out = anova2_repmeas_autodesign(data,factNames,printOutFlag)
% computes 2-way repeated measures ANOVA on data matrix: 1st dim = subjects,
% 2nd dim = factor 1, 3nd dim = factor 2.
%
% Johannes Schultz spring 2007
if ~exist('factName... |
95a8df3f953f86817ab37aa8be33406267b3db9498622ea51b60715f19ef4bad | MATLAB | 1,224 | 33 | function obj3 = binaryopp(f, obj1, obj2)
if isa(obj2, 'mmo'), tmpobj = obj2; obj2 = obj1; obj1 = tmpobj; clear tmpobj; end
if ~isequal(size(obj1), size(obj2)) && prod(size(obj2)) ~= 1
error('Matrix dimensions must agree.');
end
data1 = memmapfile(obj1.dataFile, 'writable', obj1.writable, 'forma... |
f7f538a207d81157448a9ba76f6decb50a9d8cda52861124b3f0fda745f23888 | MATLAB | 1,224 | 55 | function [cem_out,w] = cem_detector(hsi_img,tgt_sigs,mask)
%
%function [cem_out,w] = cem_detector(hsi_img,tgt_sigs,mask)
%
% Constrained Energy Minimization Detector
% solution to filter with minimum energy projected into background space
%
% inputs:
% hsi_image - n_row x n_col x n_band hyperspectral image
% tgt_sig... |
61a7014e2c0f6f4aafb3b903ef6179b806a44960f76539c20b56f8dbab7f8975 | MATLAB | 1,226 | 53 |
% Panels can be any size.
%
% (a) Create an asymmetrical grid of panels.
% (b) Create another.
% (c) Use select('all') to load them all with axes
% (d) Get handles to all the axes and modify them.
%% (a)
% create a 2x2 grid in gcf with different fractionally-sized
% rows and columns. a row or column sized as "-1" ... |
9e6cd0a6fd078f9097f8f54c4e4a17264a9c3035299360c5bd956f4a349e2f85 | MATLAB | 1,226 | 26 | function par = sero_pulseq_defaultPars()
% function par = sero_pulseq_defaultPars()
par.tShot = 0.15; % step time [s]
par.nShot = 1000; % number of shots/samples
par.nPos = 50; % number of positions/slices
par.ar = 4; % aspect ratio
par.dz = 1.5e-3; % step length in z [m]
pa... |
389ae511b0f736c373afbda994de5a674fc7f61f9eae6af5ee3acf886066bb9c | MATLAB | 1,227 | 29 | function residuals = CorrResiduals(spikes, intervals1, intervals2)
% Computes the residuals of the post vs pre pairwise spike train correlations
% using the intervals provided, as described by Giri2019 JNeurosci
% Pearson's correlation for each pair of neuron's spikes will be computed
% within intervals1 (e.g. rippes... |
e46bd05b6f44966348f94dedc713f6e0b57a63742ae07b09d45ba1e70b15e629 | MATLAB | 1,228 | 24 | %-----------------------------------------------------------------------
% Job saved on 31-Jan-2024 16:03:11 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%% load libraries, I think
run('set_library_paths.... |
15f3e7f9138b703fee1f89935fad5749ddec98e51d2277fa1521ac0fc86d3724 | MATLAB | 1,229 | 47 | function [finalParams, MSE, initCond, fitParams] = my_fit_sigmoid(x, y, iters)
%uses fmincon to fit sigmoidal to data specified by 'x' and 'y'.
%inputs: x = vector of x values.
% y = vector of y values.
% iter = iterations of random initializations. 10-20 is reasonable.
lb = [-5, 0, 0, -5];
ub = [5, 5, 3... |
6572a496aab7c6125cc8d12c970a7d2b90e6fb84c323af61bb14da237a261243 | MATLAB | 1,229 | 39 | function [ params ] = tapas_BLT_runIntroMain( params )
% tapas_BLT_runIntroMain Presents written instructions and logs the event
%
% About:
% Coded by F.Petzschner 19. April 2017
% Last change: F.Petzschner 19. April 2017
for i = 1:params.nIntroMain
Screen('DrawTexture', params.screen.window, params.text.I... |
9f0fd02b046c26e5dff073272fc904d5d18a27ebf94c1eb243398f11811dbbdd | MATLAB | 1,229 | 31 | function str = finish(str,unknowns)
%TEMPLATE/FINISH Apply given strategy to unknown fields in a string
% STR = FINISH(STR,UNKNOWNS) applies on string STR the strategy defined
% in UNKNOWNS to unknowns fields '{UNKNOWNS_FIELDS}'.
% UNKNOWNS may be:
% * 'keep' to do nothing
% * 'remove' to remove all undefined ... |
a756d1bc0ad5737adb8ad9a768deaeef4ee12ec4a2de8ff415abd36d45d6c7e4 | MATLAB | 1,229 | 37 | %% SpecifyToolboxesDirectory.m
%
% Description: Specify the toolboxes's directory
% The specificed path must contain the following directories as original one:
% MEDI toolbox - functions/
% STI Suite - Core_Functions_P/
%
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 24 August 2018
% Date modi... |
1fa10a5c13ff4a2f7bd624799b37c86651b416867c52916d248348bdcb57b1db | MATLAB | 1,230 | 32 | function [values] = modal_control(A)
% FUNCTION:
% Returns values of MODAL CONTROLLABILITY for each node in a
% network, given the adjacency matrix for that network. Modal
% controllability indicates the ability of that node to steer the
% system into difficult-to-reach states, given inp... |
2eea71935fe7e4a0b57be6bce20f6f8f5f4e43a1cf3ad7449a93670adbf1c887 | MATLAB | 1,230 | 54 | function [state] = tapas_sem_hier_init_state(data, model, inference)
%% Generate the structure of the states of the sampler.
%
% Input
%
% Output
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
nc = size(model.graph{1}.htheta.T, 2);
ns = size(data, 1);
mu = model.graph{4}.htheta.y.mu;
nb = numel(mu);... |
d96288220c1f95a87882a0886d6f2ec5b55a97f24d67749a2b797f24ce4dc6b2 | MATLAB | 1,230 | 42 | %% output = get_variable_from_headerAndExtraData(headerAndExtraData, variableName)
%
% Input
% --------------
% headerAndExtraData : structure contains any formats of the target variable
% variableName : name of the variable, string
% matrixSize : validating matrix size
%
% Output
% --------------
% outpu... |
eb4ebd42007e786d3945e8df9044bf370defa878d171eae9a80a4cc2e61a2c87 | MATLAB | 1,230 | 40 | function plotJointAngleCorr(kinematicsAll, field)
% Correlation matrices grid layout
fig;
hold on;
axis off
axis equal
% Params
cmap = diverging_map(linspace(0,1,20), colormapHSV([255,225,0]/255, [], [], 0.8), colormapHSV([0, 212, 220]/255, [], [], 0.8));
height = 50;
width = 50;
space = 15;
heights = [[height 0];[he... |
f69c1dc941d80a0ab732e013618a4e269a6ebcad576a67b367589c44189e8c52 | MATLAB | 1,230 | 43 | function [nstate] = tapas_mh_mc3_adaptive_ti_sample_node(data, model, ...
inference, state, node)
%% Samples for a particular node assuming there is a function for it.
% Fundamentally the temperature schedule is assumed to a state and not a
% parameter.
%
%
% This works as the conditional independency of the level... |
0d0a3a54944aceb7fd48128a404219453333f512c84c7985d7b8a26cf284ab2d | MATLAB | 1,231 | 37 | function [interp_cmap]=interpolate_cbrewer(cbrew_init, interp_method, ncolors)
%
% INTERPOLATE_CBREWER - interpolate a colorbrewer map to ncolors levels
%
% INPUT:
% - cbrew_init: the initial colormap with format N*3
% - interp_method: interpolation method, which can be the following:
% 'nearest' - n... |
92e28e52fe3c1d52c4792214357ec4744592f49fa6e8faf1940977f601ce926b | MATLAB | 1,231 | 32 | function [fact,unit_string] = ExponentToUnit(e,o)
% Utility function for some nice plotting of data.
%
% function [fact,unit_string] = ExponentToUnit(e,o)
%
% Receives the exponent of the largest absolute value of the data (i.e.
% log10(max(abs(data)))) and the exponent after the data is scaled by the
% exponent... |
a7ad695ac67229fd2a874e1b523893cf4da51b2b1ba9abe6ff89efa3729a8e81 | MATLAB | 1,231 | 48 | function [pressure, flow, pass] = Run_allparam_simulator(x, file_id, nv, ntp,Qdat)
%[f2,f3,fs2,fs3,alpha]%,rminScaling]
% x = x'; %comment out if doing physiolgical parameters
% f2_vec = x(:,1);
f3_vec = x(:,1);
f3p1_vec = x(:,2);
f3p2_vec = x(:,3);
f3p3_vec = x(:,4);
fs2_vec = x(:,5);
% fs... |
e63eb4efc3f37113d379fa1c0b2817521dc4795de668b3497b468ff1388fb682 | MATLAB | 1,231 | 28 | function outputs = loadDecodeAll(dataPath, datasets, kinematicField, neuralField, fitModels)
% Wrapper over loadDecode to run all models for all datasets
if nargin < 5
fitModels = [1,1,1,1,1,1]; % fit all 6 model configurations
end
% Loop
outputs = struct('mouse', cellfun(@(x) x{1}, datasets, 'UniformOutput', fal... |
334d431640ab94c3e8c06b12bd0ea8a8efa8660197687e6b924b2e87ad8e944a | MATLAB | 1,232 | 43 | function [ uint32le] = VAXF_to_uint32le(floatVAXF)
%VAXF_TO_UINT32LE Converts from VAXF (single precision) to IEEE-LE (UINT32)
A = 2; % VAX specific
B = 128; % VAX specific
C = 0.5; % VAX specific
D = log(2); % VAX specific
% Determine the sign bit. If -ve transform to positive.
S = zeros(size(floatVAXF))... |
82183756d01fa04fbb3b8b33ccc9c1cf2a01611a6c1e0c2a0a350f5e0f1b860b | MATLAB | 1,232 | 34 | function parentNode = traverseFolder(parentNode, currentFolder)
% Get all contents of the current folder
contents = dir(currentFolder);
% Filter out '.' and '..' directories
contents = contents(~ismember({contents.name}, {'.', '..'}));
[~, sort_idx] = natsort({contents.name});
content... |
d284ab3863b9ebd0c65b666523cc19cbd6ceb86dff8e1ce0ae4406e0a3513fe9 | MATLAB | 1,232 | 44 | function [sigma,shrinkage,sample]=covdiag(x,df,varargin)
% function [sigma,shrinkage]=covdiag(x,df)
% Regularises the estimate of the covariance matrix accroding to the
% optimal shrikage method as outline in Ledoit& Wolf (2005).
% Shrinks towards diagonal matrix
% INPUT:
% x (t*n): t observations on p ran... |
82ea09acdf3f16abc7ddfc2381ed6ddf7ceaed5fdcc860692ce8babdccf601ad | MATLAB | 1,233 | 49 | function[tl1,tl2]=rotatetl(h,rot,tb)
%%%%%%%%%%%%%%%%%%%% Get current graph properties %%%%%%%%%%%%%%%%%%%%%%%
a=get(h,'XTickLabel');
b=transpose(get(h,'XTick'));
c=get(h,'YLim');
if strcmpi(tb,'t') || strcmpi(tb,'top'),
tb=2;
elseif strcmpi(tb,'b') || strcmpi(tb,'bottom'),
tb=1;
else
disp('The third argum... |
a52f8a4c31c355c6448df95916e95a73fd2a744c834bc24db4574c5d28b284d3 | MATLAB | 1,233 | 42 | function f=loglike(W, S)
% LOGLIKE - log likehood function to estimate dependence between components
%
% Usage: f = loglike(W, S);
%
% Computation of the log-likelihood function under the model
% that the ICs are 1/cosh(s) distributed (according to the tanh
% nonlinearity in ICA). It does not exactly match for the log... |
a82123a8733f513324f59cf7449932e761786f751ea7d9dad0a15e8ab90dc8d7 | MATLAB | 1,233 | 47 | function EquateScales(varargin)
%EquateScales - Equalize the the x and y scales on all the axes of the current figure
% EquateScales('x') equates the x-axes only, and EquateScales('y') - the y-axes only.
%
% Copyright (C) 2020 by Ralitsa Todorova
%
% This program is free software; you can redistribute it and/or modify... |
eed055443a246dd13c6df0f310e561c9f12de9d3c70fc8db344390c97cace7d3 | MATLAB | 1,233 | 35 | function varargout = covSEvlen(llen,varargin)
% Wrapper for Squared Exponential covariance function covSE.m.
%
% Squared Exponential covariance function with spatially varying lengthscale.
% The covariance function is parameterized as:
%
% k(x,z) = sf^2 * sqrt(a/b)^D * exp(-(x-z)'*(x-z)/b) where
% a = 2*len(x... |
5cc8ca98110b48b4e864a0c9ecc49fce827f1ca388152078d49e70b953d1aa92 | MATLAB | 1,234 | 57 | function b = catuneven(dim, padval, varargin)
%CATUNEVEN Concatenate unequally-sized arrays, padding with a value
%
% This function is similar to cat, except it does not require the arrays to
% be equally-sized along non-concatenated dimensions. Instead, all arrays
% are padded to be equally-sized using the value spec... |
7ad3f8565419ca1e9cdb64dfa02299e7afa1bcb2954417e366326944bea36e86 | MATLAB | 1,234 | 36 | %% addon_config
%
% Description: Addon script to incorporate new method to the SEPIA framework
%
% Kwok-shing Chan @ DCCN
% k.chan@donders.ru.nl
% Date created: 27 June 2020
% Date modified:
%
% DO NOT change the variable names, update the variable value instead
%
%% main
% This name will be used thorough the SEPIA f... |
1855a79e5319a68fad1919610b7a86cceae29fec767b93fed5adcc76a7e54978 | MATLAB | 1,235 | 44 | %% 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
% ... |
19915d3c1ca3fb335dfdbefb208994917f97efc6f4a3a8125d928834cdb03d87 | MATLAB | 1,235 | 55 | function [model] = tapas_sem_mixed_prepare_model(data, model, inference)
%%
%
% Input
%
% Output
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
model.graph{1}.htheta.model = ...
tapas_sem_mixed_prepare_ptheta(model.graph{1}.htheta.model);
% The trick is that now njm includes also the informati... |
a89180fbdd88dd84f229539a4a9277e70c3ecac1e9f2ec6836d453a45eb53bc9 | MATLAB | 1,235 | 48 | function this = extract_rois(this, maskArray, keepExistingRois)
% Extracts data from this image for voxels within rois given by mask images
%
% Y = MrImage()
% Y.extract_rois(maskArray, keepExistingRois)
%
% This is a method of class MrImage.
%
% IN
% maskArray (cell array of) binary MrImage
% keepExi... |
190bad8d6677f915d211fb766cca12637ddaa89c5860af11d2e6eac8939677ea | MATLAB | 1,236 | 64 | function [fits] = tapas_sem_generate_fits(data, samples, model, time)
%% Generate the fits of the data.
%
% Input
%
% Output
%
% aponteeduardo@gmail.com
% copyright (C) 2019
%
CONG = 0;
INCONG = 1;
n = 3;
n = n + 1;
if nargin < n
t = data.y.t;
maxt = max(t);
mint = min(t);
nv = 300;
time = lin... |
26c0b137b25b0499ff682717d66b5036c801dfdd3c25016950153e5f5cf926d7 | MATLAB | 1,236 | 56 | %% Sept., 16, 2017
% Testing whether a retraction can be boosted into
% a higher order retraction by integration (time stepping).
% It seems yes -- there ought to be more efficient ways.
clear all, close all, clc;
%%
n = 5;
M = spherefactory(n);
x = M.rand();
v = M.randvec(x);
%%
h = logspace(-6, 0, 101);
g = ... |
5122b095eb3b52b4fa3443a22a50af0a5c25498c85c27f3ef0fbea897d054df5 | MATLAB | 1,237 | 39 | function brightenedColor = tapas_uniqc_get_brightened_color(baseColor, iStepArray, ...
nSteps, maxBright)
% brightens color for given indices by predefined number of steps
%
% brightenedColor = tapas_uniqc_get_brightened_color(baseColor, iStepArray, nSteps, ...
% maxBright)
%
% IN
% baseCol... |
c36b223f7397f7f4f7c80ff861c771555ab2d4d924fc41c042cab775f1655b0a | MATLAB | 1,237 | 55 | function [model] = tapas_sem_multiv_prepare_model(data, model, inference)
%%
%
% Input
%
% Output
%
% aponteeduardo@gmail.com
% copyright (C) 2016
%
model.graph{1}.htheta.model = ...
tapas_sem_multiv_prepare_ptheta(model.graph{1}.htheta.model);
% The trick is that now njm includes also the informa... |
e4c1838a104edf2fc6be876f1a60947c8d35efecb9ebcc40243979d8276c9397 | MATLAB | 1,237 | 29 | function [pvec, pstruct] = tapas_ehgf_transp(r, ptrans)
% --------------------------------------------------------------------------------------------------
% Copyright (C) 2012-2020 Christoph Mathys, TNU, UZH & ETHZ
%
% This file is part of the HGF toolbox, which is released under the terms of the GNU General Public
%... |
e7bd17f993fb353bb2b5ffcc001a80e18209ae099e40558c1b1995afbb6d08a8 | MATLAB | 1,237 | 36 | % Performs fast detrended fluctuation analysis on a nonstationary input signal to
% obtain an estimate for the scaling exponent.
%
% Useage:
% [alpha, intervals, flucts] = fastdfa(x)
% [alpha, intervals, flucts] = fastdfa(x, intervals)
% Inputs
% x - input signal: must be a column vector
% Optional inputs
%... |
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