sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a24fd6e2c483b45e519254c05586f866ae40a0879386e5be36a28e5a2c487758 | MATLAB | 1,944 | 64 | function walkerdots = mdComputePositions(md2D, markers, tw, speed, xcenterw, ycenterw, fr, invert);
%walkerdots = mdComputePositions(md2D, markers, tw, speed, xcenterw, ycenterw, fr)
%
%Computes the array of dots to draw as the current frame of the walker.
%Loops walker when we get to the end of the md data set
%
%INP... |
945dd5c272bf0ced74caa85d1d20ce0f6fb60ad3aa854896f20af15d35ccedbd | MATLAB | 1,947 | 50 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
07fe7ea421accff50153f0c43d076cfec0d03d143028254360e222c73ce3a435 | MATLAB | 1,951 | 56 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
9c60a787800ea0ada9d617c66f57ec8043082a1d4bf8cf620c141ee5188fd6d1 | MATLAB | 1,951 | 40 | % Demo for emmeans
clear all
% load data
load carbig
t = table(Acceleration, Cylinders, Displacement, Horsepower, cellstr(Mfg), Model_Year, MPG, cellstr(Origin), Weight,...
'VariableNames',{'acc','cyl','disp','hp','mfg','year','mpg','orig','wgt'});
% predict MPG but interested in Origin differences so make fixed ... |
fb09037685396aad8a5a8d2cd047dd638ea247e3bc67b6336f841ae98f040d3a | MATLAB | 1,952 | 57 | function orders = make_orders(num_conds, trials_per_cond, num_orders, train)
% Generates counterbalanced order of conditions.
% Written by KGS Lab
% Edited by AS 8/2014
num_trials = num_conds * trials_per_cond;
if ~train % IBC Change: training session
% check that num_conds is a factor of trials_per_cond
if (... |
7d21d3ec745af64ff1546b5611d885e73180b83ae3a65572ca4a2b7f81072dee | MATLAB | 1,954 | 50 | % Generate an n-by-d matrix R of random numbers sampled from a multivariate normal distribution,
% which will have the desired empirical mean and covariance, i.e.:
% mean(R,1) == mu
% cov(R) == sigma a d-by-d matrix
%
% From https://stats.stackexchange.com/questions/120179/generating-data-with-a-giv... |
57eaf91fc30e3a204af4e633d167269b090f2a4fa65248f85f83f8d76d299f4f | MATLAB | 1,955 | 40 | %% Demo 11 - Binomial GLMM (binary outcome, logit link)
% A binary outcome has a mean that is a probability bounded between 0 and 1, so a
% gaussian model is invalid - a binomial GLMM with a logit link is the right tool.
% Shown on the bacteria dataset (MASS): presence/absence of H. influenzae in 50
% children measured... |
085dce864e631018da1ac8db44341d2bd72f1f7accff47a5fa64a6c985f9d363 | MATLAB | 1,958 | 68 | %%
% Unpacks x without need for temporary variables. Note that it is
% possible to request less than the total number of available elements.
% [a, b, ...] = unpack({a, b, ...})
% [a, b, ...] = unpack(struct('a',...,'b',...))
%
function [varargout] = unpack(x, fieldOrder)
%----- Cell input
if ... |
114c792d3f31694930ac56fa87daadf45db632b11186f5b2b033a6db897ceb75 | MATLAB | 1,958 | 54 | function [shifted, nshift] = alignXcorr(input, maxiter)
% ALIGNXCORR determines shifts according to xcorr aligment with average
%
% use as
% [shifted, nshift] = alignXcorr(input,maxiter)
%
% This file is part of EpiCode, see
% http://www.github.com/stephenwhitmarsh/EpiCode for documentation and details.
%
% EpiCod... |
5a1438e5c8399fcc2423a0006e288eaf4dd90c15613cff4d2b6dc5442762d901 | MATLAB | 1,959 | 52 | classdef HoldoutResultsSummary
% HoldoutResultsSummary
% Aggregates summary statistics across multiple HoldoutAnalysisUnit objects.
properties
TrainAllCorrelations % [numSplits x numComponents] matrix
TrainMeanCorrelation % [1 x numComponents] vector
TrainAllAUCs_ROC ... |
8ebab810c52e5ce7971fbd5ce35ab07d23b4dda68b9b794ef1bed7113ace7863 | MATLAB | 1,959 | 94 | function out = ghm(g,h,varargin)
% GH = GHM(X,Y,{OPTIONS})
% Calculate the geometric-harmonic mean (GHM) of the absolute values
% of two variables. Optionally, calculate the weighted GHM
%
% X,Y are of any numeric class or size (must be the same size)
% OPTIONS includes the key-value pairs:
% 'weight... |
88d1e9ca0960aa27b658c84a192af87b8cf14cdaf6153ee01290fc3660abcc52 | MATLAB | 1,961 | 72 | % Clear the workspace
clear; clc; close all;
% === 1. Read Excel Data ===
filename = 'hankou/luoshan.xlsx';
sheet = 1;
data = readtable(filename, 'Sheet', sheet);
years = data.Year;
months = data.Month;
runoff = data.Runoff;
% === 2. Construct Time Vector ===
time = years + (months - 1)/12;
train_pe... |
53f1428013d6c5a459e54174ab1e950bb5a59b5acebeabeae4f3c42e1962eb79 | MATLAB | 1,962 | 48 | function Borders=setBorders(options)
% automatically set borders on the parameters based on were you sampled.
%function Borders=setBorders(data,options)
% this function sets borders on the parameter values of a given function
% automaically
%
% It sets: -the threshold to be within the range of the data +/- 50%
% ... |
27d310ce984994c94ed3c24a684e6f06bad7318341fa1e178b0fff56523dc757 | MATLAB | 1,963 | 42 | % This file is a helper function. It takes grayordinates for the volume
% part from one sample cifti file. They grayordinates are specified in 2mm
% MNI space. They are transferred to the BCI space. For this purpose, first
% we coregistred BrainSuiteAtlas1 to BCI atlas and then used the svreg map.
clear all;close all;c... |
3156f10e2a9d82b59b03b6a6e01f29afbd1098fa382f5b27764b71ff103f05a1 | MATLAB | 1,963 | 45 |
% ‘Optimizer’
%%
clc
clear
close all
%%
%%
Fun_name=“F5”; % Function name of test functions: “F1” to “F23”
SearchAgents=30; % Function name of Pelicans (INFOpulation members)
Max_iterations=1000; % maximum iteration count for Fun_name
[lowerbound,upperbound,dimen... |
53f7ee7ee232ab264e0bcaaae16d4f8315349f7ae7baa5b78b994c2182387e26 | MATLAB | 1,965 | 48 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2017 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
a720853f7bb9bb35db61141553207d58e92f4802119bcf7b6160ca4490e888ca | MATLAB | 1,968 | 71 | classdef ByteStream < handle
properties (GetAccess = public, Dependent)
bytes
end
properties (Access = private)
total_bytes uint64
segments
end
methods
function self = ByteStream()
self.segments = gadgetron.lib.list(self.cre... |
3d5f7b687d8033f0af0e3f5963afd82d76bd98ee2d1edb5a957a9c9d7f78f6b5 | MATLAB | 1,971 | 65 | function [d,dt]=formatts(d)
%
% Usage: [d,dt]=formatts(d)
%
% Helper function for CWT,XWT,WTC
%
% Brings a timeseries into a shape so that it has two columns: [time, value].
%
%
% (C) Aslak Grinsted 2002-2014
% http://www.glaciology.net/wavelet-coherence
% --------------------------------------------------------------... |
de852fddbaf8d55df7a0bc68e9d3352325f2968f1a6ee796f891fea5decb6b6c | MATLAB | 1,971 | 66 | function [count,prop,countC] = countSpots_centroid(BW, R, tbl, posPath)
count = [];
prop = [];
countC = [];
O = fieldnames(BW);
nSpots = size(tbl, 1);
disp([num2str(nSpots),' Visium spots detected'])
disp('Building spot grid')
crow = round(table2array(tbl(:, 5)));
ccol = round(table2array(... |
0ecd2613f86f9f28d1b83577f9b0f228999c45a142dbc3ef8a16049499efc3eb | MATLAB | 1,973 | 52 | function [theta, beta] = CBIG_AuthorTopic_EstimateParams(params)
% [theta, beta] = CBIG_AuthorTopic_EstimateParams(params)
%
% Compute estimates of the author-topic model's parameters (theta and
% beta) using the current estimate of the parameters of the variational
% distribution produced by the Collapsed Variational ... |
087a877362a0eae7f49105e2f5fe154d5c32d5d55157353061542e629adeb6ce | MATLAB | 1,974 | 81 | function plot_select_pairs_fig3A3B4A4B(path_extract, seizure, time_idx, plot_duration, filtered)
% On-Demand Seizures Facilitate Rapid Screening of Therapeutics for Epilepsy
% Authors: Yuzhang Chen, Brian Litt, Flavia Vitale, Hajime Takano
% DOI: https://doi.org/10.7554/eLife.101859
% Plots select pairs of seizures w... |
945b91443b7906458d23b8daf8d831f7b74dd210e036813fe06a6e2966538f0e | MATLAB | 1,975 | 84 | function [hh,ii]=nt_iplot(name)
%[hh,ii]=nt_iplot(fname) - plot data file based on index
%
% hh, ii: header info and index
%
% name: file name
%
% nt_iplot(name): just plot the data, mean removed
%
% See nt_index.
%
% NoiseTools
nt_greetings;
if nargin<1 || isempty(name);
error('!');
end
% check 'name'
if ~isc... |
fe1d8b53ce52b433a2f6058d2be3d8f7d58eec26344e7862318b7c91f1e2a9e8 | MATLAB | 1,975 | 74 | %%
function [] = democolor(makePastel, maps, picture)
if nargin < 1
makePastel = false;
end
if nargin < 2
maps = { 'hydrangea' ...
, 'terrain' ...
, 'fade' ...
, 'hot2' ...
, 'cold2' ...
, 'g... |
78881e0355d562a865c135582c89dc31ba8f775a892d297e4053dc0f5f962191 | MATLAB | 1,977 | 73 | function nt_bsplot(x,w,style,abscissa,zeroflag,rmsflag)
%nt_bsplot(x,sds,style,abscissa,zeroflag,rmsflag) - plot average with bootstrap standard deviation
%
% x: data to plot (time * trials, or time * 1 * trials)
% w: weights
% style: 'zerobased' (default) or 'meanbased'
% abscissa: use this vector as plot's abscis... |
f07b4ff6456a495e8af779dcceb46c9bd72f457e55c180888d9095acab5bb890 | MATLAB | 1,978 | 82 | function varargout = addaxisplot(varargin)
%ADDAXISPLOT adds a plot to an axis.
%
% handle_to_plots = addaxisplot(x,y,axis_number,...);
%
% See also
% ADDAXIS, ADDAXISLABEL, AA_SPLOT
% get current axis
cah = gca;
% axh = get(cah,'userdata');
axh = getaddaxisdata(cah,'axisdata');
if ... |
f969440ea7b8c078ed7c0090e522970fc3b95f9f7a78327e24459a302898ca31 | MATLAB | 1,978 | 44 |
% This example script computes spike-tiling coefficient as described in
% Cutts et al., 2014 Jneuro. This parameter is a measure of pairwise correlation
% between pairs of spike trains. Importantly for development, it is unbiased by
% firing rate (standard correlation strongly overestimates correlations between
% pai... |
ca57c9cf21e7f42cf5102b905b15f17947960a716539e4a49edc9af33a0e7408 | MATLAB | 1,979 | 120 | function demo_sigstar
% demo function for sigstar
%
% function demo_sigstar
%
% No input or output arguments.
%
%
%
rows=2;
cols=3;
clf
subplot(rows,cols,1)
barData=[2,1.2,1.9,1,2,3];
H=bar(barData);
set(H,'FaceColor',[0.5,1,0.5])
groups={[3,6],[1,2],[5,4]};
%overlay random data
hold on
for ii=1:length(barData)... |
de2901dd16e5c13e51cb94da086198e8e46d4a47aeded4374ffcbc07340dbbe3 | MATLAB | 1,979 | 51 |
% This is a sample main file that reads two grayordinate fmri files generated by bfp and outputs the synced files.
clc;clear all;close all;
addpath(genpath('../'));
g1=load('/NCAdisk/SCD_structural_analysis/BOLD_study/SCD_BOLDdata/ACTL004/func/ACTL004_rest_bold.32k.GOrd.filt.mat');
g2=load('/home/sychoi/Dropbox/SCD/A... |
f7c01eadc2c4c26b7b9cb452bc5397c35d147f06cc43407b6cbe5f606515c431 | MATLAB | 1,982 | 61 | function gen_brainordinates_alff(BSTDir, anatbasename, fmribasename,measure)
% Measure could be 'ALFF', 'ALFF_Z', or 'fALFF_Z'
%bfp_out,subid,'func',[subid,'_',sessionid
sub_mri = [anatbasename, '.bfc.nii.gz'];
subfmri = [fmribasename,'_',measure,'2standard.nii.gz'];
if ~isfile(subfmri)
fprintf('File doesn''t exis... |
a78b1edfdf1b7e7a61cabf154cf71ab5119b73461537d2c5ecaa36369874262f | MATLAB | 1,984 | 70 | function y_hat = CBIG_regress_X_from_y_test(y, X, beta, X_train_mean)
% y_hat = CBIG_regress_X_from_y_test(y, X, beta, X_train_mean)
%
% This function applies the regression coefficients "beta" generated from
% the training set (see CBIG_regress_X_from_y_train.m) to regress the
% nuisance variables X from the target ... |
7b179fd06d8d6ff1e43b1b3031cd51638d32bc7140360e4bd1d24f6c0b9e52b3 | MATLAB | 1,985 | 90 | function [C,idx]=nt_xxcorr(A,B,centerflag)
%[C,idx]=nt_xxcorr(A,B,centerflag) - true normalized unbiased cross-correlation function
%
% C: normalized unbiased cross-correlation function
% idx: index of largest extremum.
%
% A: first column vector
% B: second column vector (nsamples < A)
% centerflag: if true pad... |
593f5a0686959c1359fbcbd38531f7bc3cf57e3f3b2b0d3aa4b281af42a9a53b | MATLAB | 1,986 | 75 |
close all
load([pwd '/init_data/var_combos.mat'],'var_combos','var_vectors');
numPerBlock = 1000;
[lpp, ~] = size(var_combos);
maxNumBlocks = ceil(lpp/numPerBlock);
n_totalVars = length(var_combos)/length(var_vectors{1});
Sim_results = [];
for i = 1:maxNumBlocks
resultsi = load([pwd '/result/Sim_results' nu... |
5f9662af2bfa5aae2a4a4e8e12a3bc39250c1ca07cd3826f89fe087d35f76132 | MATLAB | 1,990 | 58 | %% main script to create field analysis gui input and calculate spatial information
main_path = "G:\";
rootdir = strcat(main_path,\CA1 miniscope data"); % change this according to your path
addpath(strcat(main_path, "Discrimination 2025 CodeBase\Spatial remapping\SpatialRemapping"))
workdir_d = [strcat(rootdir,... |
25258fa908fe825b46f11ec2c4f30367f887a05f42344e18a43fb591bb016cbe | MATLAB | 1,992 | 53 | function Tcoeff = getTCstimSingleLags(animal_name, ...
spike_matrix, lags, repeat_calc, save_data, output_folder, stim_period, clusters)
%% By Mattia 01.20
% just a wrapper for any spike-tiling coefficient function
% it is used in the example script "MainSpikeTilingCoefficient.m"
% inputs:
% - animal_name (strin... |
994e6da21a907b45fff1bdac0ae1521b9152fc4aa8112996079ab7b9bda569de | MATLAB | 1,995 | 51 | %% Function to apply field mask on each map
function [Summary_tbl, FieldMap_full, FieldMap_sess] = ApplyMask(maps, fields)
field_counter = 1;
[N_cells, N_session] = size(maps.ActivityRate_sess);
FieldMap_full = cell(N_cells,1);
FieldMap_sess = cell(N_cells, N_session);
field_ID = [];
cell_ID = [];
FieldSize = [... |
4bddf6def1b2871934e54176da4423ad7f82a46e33fa01a90455705ca92b4f91 | MATLAB | 1,997 | 61 | function [delta, theta, alpha, beta, gamma, broad_1, broad_2] = compute_bands(signals, fs)
% signals: Matrix of input signals (each column is a signal)
% fs: Sampling frequency
num_signals = size(signals, 2);
params.tapers = [3, 5];
% Define frequency band edges (in Hz)
edges = [0, 4; 4, 8; 8... |
2d4f75ff2ec3f65ccb89a9c6bacabe6d6e71f5a3a172128fbf86a85cbe5a4b92 | MATLAB | 1,998 | 79 |
dim = 128;
dim_kernel = 5;
num_th = 11;
num_sc = 10;
pad = (dim_kernel-1)/2;
mp = zeros(num_th, num_sc);
mp1 = zeros(num_th, num_sc);
cn_act = zeros(num_th, num_sc);
cn_no_act = zeros(num_th, num_sc);
Jaccard = zeros(num_th, num_sc);
KL = zeros(num_th, num_sc);
JS = zeros(num_th, num_sc);
RMSE = zeros(n... |
9f2b52698e2c3bfe1084dfeec8492c8aec6211c9af1e63d7fa2366de9578fedc | MATLAB | 1,998 | 66 | %% ========================================================================
% Analysis_IOI.m
% Intrinsic Optical Imaging pipeline:
% 1) Normalize data
% 2) Rearrange frames by cycle phase
% 3) PCA + Indicator Function method
% 4) Reconstruct cleaned data
% 5) FFT retinotopy maps (phase + amplitude)
% =... |
3830e7663989e4b24c61878ff91addeb38083cddfc621c428da9528aad42196c | MATLAB | 1,999 | 58 | function Happ = bilin_Hessfun(x, lambda, S, Y, A, h, opt)
% function [fun,varargout] = bilin_Hessfun(S, Y, A, h, D, opt)
%
% Function to calculate hessian multiplication function
% for 'HessianMultiplyFcn'
%
%
% calculate Hessians
% First term dS 2*vec((H^T*H)*S*(A*A^T)) = 2*kron((A*A^T),(H^T*H))
% Second term dS... |
792b6f13c1c00530a0b74a09fb94483f6e98bf15090581ffa1774904c5564a87 | MATLAB | 2,001 | 46 | function dtx_spikes_writeSC(ipatient)
if ispc
addpath \\lexport\iss01.charpier\analyses\lgi1\Git-Paul\fieldtrip;
addpath (genpath('\\lexport\iss01.charpier\analyses\lgi1\Git-Paul\EpiCode\projects\dtx'));
addpath (genpath('\\lexport\iss01.charpier\analyses\lgi1\Git-Paul\EpiCode\external'));
addpath (gen... |
433d006e1b0eb2fd10c42e90a79652d1d60c7393564cb85163eff9f559445439 | MATLAB | 2,002 | 44 | function preictal_spikes_slurm_joblist
%find config script :
addpath (genpath('\\l2export\iss02.charpier\analyses\vn_preictal\scripts\EpiCode\projects\preictal'));
config = preictal_setparams;
sc_version = '1.0.8';
fname = fullfile(config{1}.datasavedir,'preictal_slurm_job_list.txt');
fid = fopen(fname,'w');
for iel... |
4c03085b927392d3805a8e17ce8cbb88fac63635a6f081c081ef0ceee5d62497 | MATLAB | 2,003 | 42 |
function bytes = encode_image_headers(headers)
nheaders = numel(headers.version);
bytes = zeros(198, nheaders, 'int8');
function bytes = byte_view(array, width)
bytes = reshape( ...
typecast(squeeze(reshape(array, 1, [])), 'int8'), ...
width, [] ...
);
end
... |
fdb99edf0ab8a2967dc67cd55b11184cfe24c10ef384106f943d5aa554cd50a8 | MATLAB | 2,005 | 66 | function I = gcmi_mixture_cd(x, y, Ym)
% GCMI_MIXTURE_CD Gaussian-Copula Mutual Information between a continuous and a
% discrete variable in bits calculated from a Gaussian mixture
%
% The Gaussian mixture is fit using robust measures of location (median) and
% scale (median absolute deviation) for each... |
07cb68734db0f2154e5ecfa1c8c775a812624439f2077bfcd3bb8168de8c6e04 | MATLAB | 2,006 | 80 | function outpict = zblend(inframes,mask)
% ZBLEND(INFRAMES,MASK)
% use a mask to blend between multiple images in a 4-D array
%
% INFRAMES is a 4-D image array (I/IA or RGB/RGBA)
% MASK is an image representing depth in the image stack
% can be a single image (I or RGB)
% can also be defined... |
2cf33fdcacd4b013a1940b12015709751345c498274c98bdefc713a6b0eb1ba5 | MATLAB | 2,009 | 39 | function [devianceResiduals,deviance,samples_deviance,samples_devianceResiduals] = getDeviance(result,Nsamples)
%function [devianceResiduals,deviance,samples_deviance,samples_devianceResiduals] = getDeviance(result,Nsamples)
% This function calculates the observed deviance from the model.
%
% If you ask for more than ... |
f6ca48d21c51a882b3c27f3f25786bcc2857e0b8752fc9ddde33d0fcd77fde5f | MATLAB | 2,018 | 84 | function [Xt, Yt, Zt, maxk]=filter_PFs(Xt, Yt, Zt, maxk, smoothwind,stype, addwall, rtips, mode)
J=length(maxk);
% add arificial MT-wall part
if addwall>0
wallsize=addwall;
Xwall=0.0001*ones(wallsize,length(maxk));
if mode == 1
Ywall=0.0001*ones(wallsize,length(maxk));
end
Zwall=[];
... |
ce8551d28e5634614aacd027c43841c1294d1d79de9a5d4b424676850c2c86bb | MATLAB | 2,026 | 45 | function spike_matrix = getMUASpikeMatrix(animal_name, ...
resultsMUA, output_folder, save_data, repeatCalc, area)
% by Mattia 03.21
% computes spike_matrix with 1ms resolution, starting from the output of
% detected MUA timestamps (e.g. when no SUA is available/needed)
% if you would like to have all your MUA s... |
32a3e1c6340a06d26f0833799a4dde52b5a0e2b855c568ba1666fc5a82f44c37 | MATLAB | 2,027 | 39 | %function startup
% on startup setup the java class path for the stuff here
set(0,'defaultaxesfontsize',14);
% sets up path to use usb2 java classes
disp 'setting up java classpath for jAER interfacing'
% here=fileparts(mfilename('fullpath'));
% % jars are up and down from us
% p=[here,'\host\java\'];
% javaa... |
90a3d6bec9988c85695af0aafc62c02d212e0b4bf5ad9198fc983a0a9ffadac0 | MATLAB | 2,027 | 75 | function [cfg, LFP] = alignTemplates(cfg, LFP)
cfg.orientation = ft_getopt(cfg, 'orientation', 'landscape');
t = [-0.15 0.10];
% t-zero LFPs
fig = figure;
papersize = 800;
set(fig, 'PaperPositionMode', 'auto');
if strcmp(cfg.orientation, 'landscape')
set(fig, 'position', [20 -60 papersize*sqrt(2) paper... |
bc73ceff816d9f8b0b7a1d48e613120f82c529d220d8e2bc822ad9433386bc1f | MATLAB | 2,029 | 57 | function [Params] = read_params(suffix);
% Reads parameters passed by grab
%
param_file = ['Parameters', suffix];
if ~isfile(param_file)
error('Params file does not exist!!')
end
fid = fopen(param_file);
data_lines = textscan(fid,'%s','Delimiter','\n');
fclose(fid);
if numel(data_lines{1}) ~= 3
error('Expecti... |
fefd73d2ff9790879531de097cfbd8881313a50266e7d31a1f50e9e78ef7a907 | MATLAB | 2,029 | 63 | function featval = moving_window_feature_calculation (input_data, fs, winLen, winDisp, featFn, varargs)
% On-Demand Seizures Facilitate Rapid Screening of Therapeutics for Epilepsy
% Authors: Yuzhang Chen, Brian Litt, Flavia Vitale, Hajime Takano
% DOI: https://doi.org/10.7554/eLife.101859
% Function Purpose Calcula... |
5e6f374b6c719b1e7f6c3d343b5f936da6bbe487e7bcbe201cfacb24afe682c2 | MATLAB | 2,031 | 53 | function createBAT(animals, BATfolder, PRMfolder)
% by Mattia. creates the lynux script that you can use to run clustering on
% all your files.
% INPUT:
% animals - see main script, you can easily rewrite it with
% experiments if this suits better your needs
% BATfolder - string, where yo... |
9b258c13ce308fb6211278d8e3722f9a46162840ff1919699d632ef007101bea | MATLAB | 2,031 | 48 | function recon_data = read_recon_data(socket)
recon_data = gadgetron.types.ReconData(read_recon_bits(socket));
end
function recon_bits = read_recon_bits(socket)
n_recon_bits = read(socket, 1, 'uint64');
recon_bits = arrayfun(@(~) read_recon_bit(socket), 1:n_recon_bits);
end
function recon_bit = read_recon... |
3748c57f13eefb4d4e4d1e6b90f82f64b110c075f598980272bb7b31f60d3cc3 | MATLAB | 2,033 | 43 | %% function to count events - 2nd version when maps and eventXY has the same cells included only%% Function to count Ca events in individual fields
function [EventCounter, FieldEventTime, FieldEventPercentage] = CountFieldEvents_MisMatch(FieldMap_full, onset, p)
EventCounter = [];
FieldEventTime = {};
FieldEventP... |
dd3c82ce7fd218142ab317759cae446af5763daaf6b68be0ad84253442641097 | MATLAB | 2,034 | 76 | function outpict = colorbalance(inpict,K,preserve)
% OUTPICT = COLORBALANCE(INPICT,K,{PRESERVE})
% Shift the color balance of an image. This is based on the legacy GIMP tools.
%
% INPICT is an RGB/RGBA image of any standard image class.
% Multiframe images are supported.
% K is the parameter array. This is a 3... |
ebbb4b140f1a4290f2be83884f03dcc9bfe05e36d4067d07ceae1da743dacfde | MATLAB | 2,034 | 27 | function KCresponse = calculateKCresponse(MBmodel, PNactivity)
%% refers to the spiking/output activity of KCs, incorporating APL inhibition and spiking thresholds
% expects MBmodel to have the weighted connectivity matrix PNtoKC, alpha
% (APL gain) and C_theta (scaling for thresholds). PNactivity expected to
% be M-by... |
2042fabc45e4e4a0e0ea29e6a762b6af73b6a6a28794bb7084d3b48116de3cfe | MATLAB | 2,043 | 67 | % use mc_untidst_wouter_dante.m
% ATTENTION: this program is needed to remomve NAN values from the to GRE
% registered MASK:
% STEP1a: Do Coreg.Estimate Reslice in SPM (with
% GRE(Reference),Anat(Source), and Mask(Other)
% STEP1b: before using mc_undist_wouter_dante.m: here.
clear
% addpaths
addpath('/fmri/apps/spm5'... |
629ef82af82627b98996c169fe9c4ecf1d50476016427903ffc6478b9e3b6acb | MATLAB | 2,043 | 79 | function c = bipolarcmapW(varargin)
% Returns an approx. bipolar colormap centered at zero (in cRange). Zero
% maps to white.
%
% method is type of interpolation to be used. It can be
% ['sigmoid'], 'linear', 'quadratic', or 'cubic'
%
% colors is the color combination to be used for +ve and -ve part. It can be
% ... |
2bd7e747a4ad3fd80c4d6261ae0fc63b6e22f6476ce9d9d52e962d5577ac5f57 | MATLAB | 2,047 | 60 | function tform = get_electrode_positions(datarun,epi_image)
% get transormation matrix from fgp_array image to matlab electrode
% locations
% usage: tform = get_electrode_positions(datarun,epi_image)
%
% arguments: datarun - datarun structure
% epi_image - array_GFP image
%
% outputs: tform - ... |
8c51ba35e386cc0e87ac74b8ca19a7d7d5322c8c9e24e7f9a05455dfbbe27efa | MATLAB | 2,050 | 46 | function plotInterictalPeaksV2(Number,IIA_batchResults)
length = size(IIA_batchResults{Number, 1}.OriginalSignal);
threshold = zeros(length(:,1),1);
for point = 1:length(:,1)
threshold(point,1)=IIA_batchResults{Number, 1}.threshold;
end
thresholdMatrix = [IIA_batchResults{Number, 1}.OriginalSignal(:,1) threshold]... |
f5a313a2407c4cb8641f0b163c23b97df8d6ab28381c8843898960106244f3bc | MATLAB | 2,052 | 79 | function [outpict,varargout] = imreadort(fname)
% OUTPICT = IMREADORT(FILENAME)
% [OUTPICT MAP ALPHA] = IMREADORT(FILENAME)
% Read an image from an image file and reorient it based on
% available EXIF metadata. If no orientation tag exists,
% image will be returned as-is.
%
% While this tool is intended for use... |
6bc5664a9cf220101162863d3018ced9402ee0fc19fe3ff356b4ab4396a22a66 | MATLAB | 2,053 | 42 | %% wrapping function for gui input and spatial info score
function SpatialInfo = Wrap_SI(workdir,discrimination)
SpatialInfo.Individual = cell(length(workdir),1);
SpatialInfo.Cohort = {[]; []};
SpatialInfo.All = [];
filterSize = 1.5;
framerate =30;
for f = 1:length(workdir)
clearvars -except SpatialInfo... |
a9b2668651ee55fc89836c0a6aba644069dddb1ab3057480decc3d22947ee266 | MATLAB | 2,056 | 80 | close all; clear all; clc
addpath(genpath('/data/code/matlab'));
prepOutput;
%%%% PARAMETERS %%%%
% Database
database{1} = '/data/coord/tyr/tyrunits';
database{2} = '/data/coord/zen/zenunits';
% Data files
dataDir1 = '../data/cohLFP_TestJustPrintComplex';
dataDir2 = '../data/cohLFP/_old2/500ms_5Hz_Target';
% Displ... |
d4b5edc52a2f18963856c0a255799df9cd08fdfc101263f5f2546ac519e9ed0a | MATLAB | 2,057 | 60 | function [ ] = generatePRT( PRTParameters , PRTConditions , runName , outputFolder )
%outputFolder = fullfile(pwd,'PRTs_AF');
if ~exist(outputFolder,'dir')
mkdir(outputFolder);
end
outputFileName = [ runName '.prt'];
% --- Create new file using parameters
prtFile = fopen( fullfile(outputFolder,outputFileName)... |
d68546be500f72d05a35bd5a0bea1f8e528ad07f5b71f2ffa971883c540198ac | MATLAB | 2,060 | 52 | function [slope, intercept] = getLFPslope(power_spectrum, freq, freq4slope, to_plot)
%% Calculate power law decay exponent (1/f slope)
% By Mattia, based on Gao et al., 2017: Inferring synaptic excitation/inhibition balance from field potentials.
% INPUTS:
% power_spectrum: ´ vector of LFP power as e.g. in the o... |
2fb4c442623bbba06be6cf8bb89be32b15c29bc944d0014985a86b1e0b145750 | MATLAB | 2,062 | 33 | function handles = whiskerplot(boxQuantiles)
%% Default arguments
if nargin < 2 || isempty(boxQuantiles)
boxQuantiles = [0.09 0.25 0.5 0.75 0.91];
end
%% Plots combined across layers
levels = accumfun(2, @(x) quantile(x,cfg.boxQuantiles)', shapeVar{iVar}(iLayer,:)... |
35fbe68b056fad2feb8c0db7239a2bf5905be983c36e833cf5c3f2cdc58abf9b | MATLAB | 2,062 | 66 | function outpict = joinalpha(outpict,alpha)
% OUTPICT = JOINALPHA(INPICT,ALPHA)
% Concatenate color and alpha channels as split using splitalpha().
% If the given image already has alpha content, mix it with the new alpha.
%
% INPICT is an I/IA/RGB/RGBA/RGBAAA image of any standard image class
% ALPHA is an I/RGB ... |
5dd1889d761b81feb5debaaf4fb5a1e99d808f0b5da3ebede928b3e5e04889b9 | MATLAB | 2,067 | 73 | %
% BDP BrainSuite Diffusion Pipeline
%
% Copyright (C) 2019 The Regents of the University of California and
% the University of Southern California
%
% Created by Chitresh Bhushan, Divya Varadarajan, Justin P. Haldar, Anand A. Joshi,
% David W. Shattuck, and Richard M. Leahy
%
% This program is free sof... |
b0a0b6e120a7fdde2512435477b843da472331dcd8fdb049d552a11141be1369 | MATLAB | 2,067 | 46 | function priors = getStandardPriors(options)
% sets the standard Priors
% function priors = getStandardPriors(data,options)
% The priors set here are the ones used if the user does supply own priors.
% Thus this functions constitutes a way to change the priors permanently
% note here that the priors here are not normal... |
d4666a77fdf1028ff282a8ec18eb8ad9f9c60a3c4f93f411a5f312c1c7dcb277 | MATLAB | 2,067 | 73 | function [CMI I] = gccmi_ccd(x, y, z, Zm)
% GCCMI_CCD Gaussian-Copula CMI between 2 continuous variables conditioned on
% a discrete variable.
% [CMI I] = gccmi_ccd(x,y,z,Zm) returns the CMI between two (possibly
% multidimensional) continuous variables, x and y, conditioned on a third
% discrete vari... |
a94233de80492482e55bb8d923c6c139d4bd5bd8c624b6914062c74e5c2f692e | MATLAB | 2,069 | 56 | function [AG03EEG11] = importfile_dateBS(filename, startRow, endRow)
%IMPORTFILE Import numeric data from a text file as a matrix.
% AG03EEG11 = IMPORTFILE(FILENAME) Reads data from text file FILENAME for
% the default selection.
%
% AG03EEG11 = IMPORTFILE(FILENAME, STARTROW, ENDROW) Reads data from rows
% ... |
afcef18ed9d6aacf176b92cda690408b9f9ac3be085241e61286df5959bdc9c7 | MATLAB | 2,070 | 76 | %% function to calculate heading direction relative to the most northern corner of the maze
function [HDir, Rew, RefPoint, rotXY, theta] = GetHeadingDirection(XY, event, filtSize)
[RefPoint, rotXY, theta, Rew] = GetReferencePoint(XY,event);
% calculate heading-direction
filt_XY(:,1) = movmean(rotXY(:,1), filtSi... |
3f9cd9a7e57523d983c78e926467ef6f2756e29b6217639b78a6e6bf5840b60b | MATLAB | 2,072 | 55 | function [fcnName, inputs, outputs, varLength, isInside] = parseFunctionSignature(hDocument)
%% Find the function definition indicated by the document's caret position
% If the user has placed the caret just before a function definition (i.e. only separated by
% whitespace), then use that function; oth... |
bcae54a73cfbfb54dbdf17c9c096924d47a241355f9b9300549b2e639390211d | MATLAB | 2,072 | 68 | function H0 = kbcontrasts_wald(fitmodel, emm, L)
% Hypothesis testing using Wald t/Z-tests on specified joint coefficients
% (i.e. on input contrasts)
% Copyright 2019, J. Hartman, Cornell University
% % written using Matlab version R2016a
% 2023-09-29: Modified by Kim Boström to have the output structure also
% incl... |
2b45debf8ab4d23de584361e29f50d6a66d2d7afd6ca68e7c89b1a9ebb910a57 | MATLAB | 2,073 | 54 | % RNDORTHOGONALMATRIX Generate a random m-by-n matrix R with orthogonal columns, i.e. R^T R = I.
%
% Inputs
% ========
% sz : The desired size of the output matrix, i.e. [m n ...] where additional indepdently
% generated slices (3rd and higher dimensions) can also be requested.
% A : An op... |
7ca93d62f7854bfee2f73e10606bc337c81a7fc946d6d75b057bc05c8613aceb | MATLAB | 2,087 | 67 | function [] = plim(varargin)
% PLIM Plot limits setting function.
%----- Input parsing
narginchk(1, inf);
handle = [];
iArg = 1;
axisRange = cell(1, 3);
numRanges = 0;
while iArg <= nargin && ~ischar(varargin{iArg})
if ishandletype(varargin{iArg}, 'axes')... |
8409008ca3886bb32cbc82a90e17e7385b563061b234928742434f99879f9c14 | MATLAB | 2,087 | 44 | function PPIparams = get_PPI_params(header)
PPIparams.measID = header.measurementInformation.measurementID;
PPIparams.accPE = header.encoding.parallelImaging.accelerationFactor.kspace_encoding_step_1;
PPIparams.acc3D = header.encoding.parallelImaging.accelerationFactor.kspace_encoding_step_2;
lUserParamValues = [he... |
2db44ed7c6bc0b493eadd281c77e20ed15823865e5fbb0d15db6905b525117c7 | MATLAB | 2,088 | 69 | function [counts centers] = imhistFB(inpict,varargin)
% [COUNTS BINCENTERS]=IMHISTFB(INPICT,{NBINS})
% Calculates the histogram counts for an image. If called with no output arguments, a stem plot
% will be generated for visualization.
%
% This is a passthrough to the IPT function imhist(), with an internal f... |
76ba06cd4e08a8c5911cf7b1b0f8b35ff9a2ea0a70f4fe881e63aadc2c323850 | MATLAB | 2,088 | 79 | % SVReg: Surface-Constrained Volumetric Registration
% Copyright (C) 2016 The Regents of the University of California and the University of Southern California
% Created by Anand A. Joshi, Chitresh Bhushan, David W. Shattuck, Richard M. Leahy
%
% This program is free software; you can redistribute it and/or
% modify ... |
e576c8a776087e229d2cb46d3ad3b3bb91709bf8ab4de54c2d9935cbbee041be | MATLAB | 2,091 | 67 | function patches = construct_patches(sizY,siz,overlap,min_size)
% constructs the coordinates of the different patches for batch processing
% INPUTS
% sizY: size of input data (excluding time dimension)
% siz: size of each patch (default: [32,32,4], if third spatial dimension is present)
% overlap: a... |
8e993e03ed1ab4813d2fc61c88d15300ae9069a46d84f63573a6f9bc98827fdd | MATLAB | 2,094 | 68 | function C = C_matrix_2D(x, varargin)
% Function that calculates the C matrix.
%
% Input parameters:
% --x: N1 x N2 x Nc Nyquist-sampled k-space data, where N1 and
% N2 are the data dimensions, and Nc is the number of
% channels in the array.
%
% --tau: Param... |
c8d53788fc35bf2f91f1874d08af6284be52bdbfc0eecc9935bda690b667d957 | MATLAB | 2,094 | 61 | function dummyPRF = cpm_dummy_prf(U, options, TR, nscans)
% % cpm_dummy_prf, creates a PRF struct using only inputs, options and number of
% samples. Mostly a utility tool for simulations.
%
% U - Experimental stimulus timing (see spm_prf_analyse.m for details).
% options - struct including options, most important... |
3667d79209f10df01869a0adcd90a7c1a198c93f222a2c5821d4dc8ab9cf59ad | MATLAB | 2,098 | 58 | %% Gergely Tarcsay, 2024. Assign camera frames to different behaviorally relevant states
function [States, TrialFrames] = AssignFramesToStates(event, v, v_thresh)
% assign frames whether mouse is running (1) r resting (0)
States.Run= v > v_thresh;
States.Context = zeros(length(v),1); % 1 or 2; not assigned (tr... |
5154c8a470052ec5cc42f75975d0bbcde6a658acb8b3fccf107302814071fa59 | MATLAB | 2,098 | 59 | function [D, S, graphK] = combineDictionaryPatches(RESULTS, n_patches, patches, sizY, K)
fprintf('Combining results from different patches... \n');
cnt = 0;
d = prod(sizY(1:end-1));
S = sparse(d,n_patches*K);
MASK = zeros(sizY(1:end-1));
for i = 1:n_patches
patch_lin_idx = patch_to_linear(patches{i}, sizY)... |
fdb087d077b5ee91efc3efd4be78fb3e67a392ee81a9fac2c6656d147aa866c1 | MATLAB | 2,098 | 45 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
71ba7b3e0ab0180c14790b0bb80bb8afe8d3afcde9eec76fe879137079eae32f | MATLAB | 2,100 | 43 | function dtx_spikes_slurm_joblist
%find config script :
addpath (genpath('\\lexport\iss01.charpier\analyses\lgi1\Git-Paul\EpiCode\projects\dtx'));
config = dtx_spikes_setparams;
sc_version = '1.0.1_dev';
fname = fullfile(config{1}.datasavedir,'dtx_slurm_job_list.txt');
fid = fopen(fname,'w');
for ipatient = 1:size(c... |
75f4525f21b022eb31861839eb251c73375547e7c67a31ba2e019298e89f22ca | MATLAB | 2,101 | 31 | function setpaths
restoredefaultpath
if isunix
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/git/fieldtrip
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/projects/hspike/
addpath /network/lustre/iss01/charpier/analyses/stephen.whitmarsh/EpiCode/shared/
add... |
cc234f803d89b6fe544bd68865c0836912741e3242f8e00035881b3f72506248 | MATLAB | 2,104 | 63 | function outpict = rotateds(inpict,numframes,blurcycles,shiftcycles,maxblur,maxshift,shiftphase)
% ROTATEDS(INPICT, NUMFRAMES, BLURCYCLES, SHIFTCYCLES, {MAXBLUR}, {MAXSHIFT}, {SHIFTPHASE})
% cyclically shifts the rows and columns of each channel in INPICT while simultaneously
% performing cyclic spatial ... |
fbe0366369cd050993d690800c30bf9b6e2d15a1cbd25d672496e424875c76dd | MATLAB | 2,105 | 97 | function outpict = brline(outsize,vertices)
% MASK = BRLINE(OUTSIZE,VERTICES)
% A simple tool to draw a non-antialiased polyline as a logical image.
% This is fairly crude Bresenham line tool, but I'm considering this as
% a placeholder. I hope to someday replace xwline() and brline() both when
% I get aro... |
3ad2d81ccf3613dd4388efebfa6e1ed789060c51738b0e548da095eae3b3f49e | MATLAB | 2,109 | 69 | function [A B] = matchframes(A,B,varargin)
% [A B] = MATCHFRAMES(A,B,{EXPANSIONMODE})
% Given two potentially multiframe images, expand single-frame inputs
% as necessary when framecounts mismatch.
%
% A,B are images of any class, geometry or channel arrangement.
% If framecounts differ, the shorter image will... |
ac44a7107d69391aae48070b15899645e263e79518f2706089bc60a075b44c3b | MATLAB | 2,111 | 84 |
%%
% plot
function [x,y,f] = CEC2005_plot(func_name)
[lb,ub,dim,fobj]=Get_CEC2005_details(func_name);
switch func_name
case 'F1'
x=-100:2:100; y=x; %[-100,100]
case 'F2'
x=-10:0.1:10; y=x; %[-10,10]
case 'F3'
x=-100:2:100; y=x; %[-100,100]
case 'F4'
x=-100... |
6920735af81c9e22905302806e50e9401ab25a5c979c9368fefbdd3fb2968b66 | MATLAB | 2,116 | 89 | function [y,z,mask]=nt_eyeblink(x,eyechans,nremove,sr)
%[y,z,mask]=nt_eyeblink(x,eyechans,nremove) - project out eyeblinks
%
% y: clean data
% z: eyeblink components
% mask: mask used to weight eyeblink intervals
%
% x: data to clean (time X channels)
% eyechans: ocular channel numbers, or eog signals
% nremove: ... |
9854135d5c180768ba9ffebfa7858fc4548b2efabd265a79e913303d2189bb0c | MATLAB | 2,117 | 66 | function trials = CreateTrials(walkerindex, walkerdir, walkerori, walkercoh, masktype, maskdir, maskori, maskcoh, rep)
%Randomization of trials
ran = 2; %in blocks
%rep = 4;
%Prepare trials
tr = 1;
for l=1:rep
for m=1:size(walkerindex,2)
for n = 1:size(walkerdir,2)
for o = 1:size(wa... |
9b5530f0c0d4c2bfd797e62531a3ec17977379c7fb206fdd9ad12d2ab56ad4f2 | MATLAB | 2,119 | 54 |
function plot_ei_over_epi(data, cid, im2, tform, varargin)
% map cells over epi image
% usage: plot_ei_over_epi(data,reachr_id,im2,tform, opt)
%
% arguments: data - datarun structure
% cid - id for plotting
% epi_image - array-GFP image
% tform - transformation matrix (LO... |
4d8ed30c8dac50cee664496bc47de78fd6fcc309cd94e6910678fb88b25b828d | MATLAB | 2,123 | 55 | function [distance_maxs, distance_mins, maxs, mins, types] = find_nearest_distances(all_2_find,latencies, taps)
%% Find nearest predicted peak before and after all taps or predictions
%
% **Usage:** [distance_maxs, distance_mins, maxs, mins, types] = find_nearest_distances(all_2_find,latencies,taps)
%
% Input(s):
% -... |
f169668d0a5a470dfbbdbe204770e5207a8fd8e7c9773518ab502c84ff707c04 | MATLAB | 2,123 | 52 |
Alpha Evolution: A simple and powerful optimisation algorithm to advance optimisation beyond metaphors
**************************************************************************** *****************************
% ‘Optimizer’
%%
clc
clear
close all
%%
%%
Fun_name=“F8”; % Function names: “F1” to “F23”
Se... |
b18e23c3fbc2c9f138e53e5c403901f562c4ec362f2f891619794477f6ad9ab3 | MATLAB | 2,127 | 76 | function out = orddither(img,ksize,cmode)
% ORDDITHER(INPICT, {KSIZE}, {COLORMODE})
% multilevel ordered dither inspired by Cris Luengo's blog posts
% http://www.crisluengo.net/index.php/archives/355
% and by work from others
%
% INPICT is a 2-D intensity image
% KSIZE is the size of the Bayer coeffic... |
082ba131f10127ab97054c2eb438f53ddd75d475d62753d3b4dba8168c602cff | MATLAB | 2,129 | 47 |
Alpha Evolution: A simple and powerful optimisation algorithm to advance optimisation beyond metaphors
********************************************************************************* ************************
% ‘Optimizer’
%%
clc
clear
close all
%%
%%
Fun_name=“F6”; % Function name of test functions: “F... |
87094bfe271cf8eb2e44a9f38dc6c81c190cc09244391493f0c4067a4ce18aa0 | MATLAB | 2,131 | 56 | function Y = adjustAutocorr(X, aFcn, nFFT, nParams)
if nargin < 4 || isempty(nParams)
nParams = size(aFcn,1) - 1;
end
outSize = size(X);
X = remould(X,3);
%% Original autocorrelation
Xacorr = fastAutocorr(X, [], nFFT);
Xa... |
5473254e509636644689f369f03a78fe7a4da706eb960d770ccbb4619c493c3f | MATLAB | 2,132 | 73 | %% Gergely Tarcsay, 2022. Function to parse data into individual trials and get timestamp when mouse triggered the hidden zone.
function [TrialStart, TrialStop, ZoneTriggered, context] = ParseTrials(event)
flags = event{:,1};
%loop on flags to find the beginning of the the trials, get the indicies in
%the... |
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