sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c0d269cbe337baf1d56e21a7bf3e7189f072dd58223ef80a64dfaab1a8f3815f | MATLAB | 1,307 | 50 | function [ hFig, hAxes ] = CreateRenderingFigure(varargin)
%CREATERENDERINGFIGURE Create the figure used to render meshes
%WindowSize - Size of window, tuple
%Renderer - Renderer to use, string
%ReverseZ - bool, if true reverse the Z-axis
WindowSize = [0 0 1024 768];
renderer = 'opengl';
ZD... |
15c84b38d3f49be222c264521da0c80396373fe147f3e314baee57120a203ff9 | MATLAB | 1,308 | 40 | function folds = createFolds(cfg0, G)
% [folds] = createFolds(cfg, G)
% Divides trials into folds for cross-validation. The function attempts
% to divide the trials as evenly as possible over the number of folds,
% while trying to balance the different conditions as much as possible.
%
% cfg Confi... |
3395c99aa4688474b0adadc74a49231f9747a7b9ac79371df47f78a322dcfa95 | MATLAB | 1,308 | 48 | function [h] = setAxisHandle(h, colorToBlack, xtickMinor, ytickMinor, position)
% SETAXISHANDLE Setting for figure axis
% Author: florian drawitsch<florian.drawitsch@brain.mpg.de>
% modified: Ali Karimi <ali.karimi@brain.mpg.de>
if ~exist('colorToBlack','var') || isempty(colorToBlack)
colorToBlack = 1;
end
if ~exi... |
492f20d02031a1e34524c2156fe914f72ac42fcd941f3a032c0c85cf822d00d9 | MATLAB | 1,309 | 47 | function SCM_rotationNumber(i_z,simPar)
%%% Computes and saves the rotation number of the sine circle map across
%%% natural frequencies and stimulation amplitudes for a given dithering level.
%%% The name of the output file is based on the dithering level index.
%%% 26-01-23 first commit
aVect = l... |
69aa319be94f6af105eaf298bbc8fd6c2632e20f9d7731931311cba0d58236f2 | MATLAB | 1,311 | 50 | function checkSensors(bits, vars)
%
% This function checks the value of the bit inputs to the RM1, and also the
% parameter tags known as licks. Licks indicate when a sensor has been held
% for the minHoldTime.
%
global DA gf h
for j = 1 : length(bits)
bit = bits(j);
variable = vars{j};
... |
d26dd26ac0403b6116376db5e10ec82c3101dc56f74460c33e8800667af14517 | MATLAB | 1,311 | 68 | function med = circ_median(alpha,dim)
%
% med = circ_median(alpha)
% Computes the median direction for circular data.
%
% Input:
% alpha sample of angles in radians
% [dim compute along this dimension, default is 1, must
% be either 1 or 2 for circ_median]
%
% Output:
% mu mean... |
56363abc671bb54db0f6f78dacf67e60a3c25914adfe3afab56c2a972d332302 | MATLAB | 1,317 | 96 | % Verts = [0 0 0;
% .5 0 0;
% 5 0 0;
% 0 .5 0;
% 0 5 0;
% 0 0 2.5;
% 0 0 4;
% 2 0 4;
% 0 2 4;
% 0 -2 4;
% 6 6 6]
%
%
%
% Links = [1 2;
% 2 3;
% 1 4;
% 4 5;
% 6 7;
% 7 8;
% ... |
30d9d8019c98e8a758764ef68e2ad0754ca361c46e17d8871d5484cf7da5f717 | MATLAB | 1,318 | 53 | function [results] = scaleDWB2(results, params, addPriorForWB, precomputedPortion)
% i.i.d non-mean Gaussian over spike history coefficients & constant
K = size(params.B,1);
w_sig_idx = 1;
b_sig_idx = 2;
H = double(params.H);
%w_mu = H(w_mu_idx);
log_w_sig = H(w_sig_idx);
%b_mu = H(b_mu_idx);
log_b_sig = H(b_sig... |
ae3bb076bca21c6ae807b197d90f78a3085e8fd4c629d9faabf5955e77a4d570 | MATLAB | 1,318 | 38 | function [results] = GMLMprior_spkHist(params, results, spkHistPrior_setup)
% i.i.d zero mean Gaussian over spike history coefficients, improper uniform over baseline rate terms
H = double(params.H);
%% log hyperprior
if(isfield(results, 'dH') && ~isempty(results.dH))
[lp_H, results.dH(:)] = DMC.priors.halfTPrior(... |
b7907f8103da35a91f3a996e7752195ffc4fe732d249727d4c78ba904c78538f | MATLAB | 1,318 | 50 | function [expectation,unscaled_expectation,p] = theoretical_spiking_expectation_3D(raster, x_window, y_window, time_window)
motif_order = [
1
2
3
2
3
2
3
3
3
3
3
3
... |
ea2e64737914cb8700dc771d2dfb138c3f0ec45ea26d323feebf371b276bb9e9 | MATLAB | 1,319 | 35 | function plotPerformance_SpatialMask_SNR_bar
[dataDir, options, c, d] = import_settings()
% For each ferret
files = dir( fullfile(dataDir,'*.mat'));
for i = 1 : numel(files)
[COctrl, COcool, SPctrl, SPcool, SOctrl, SOcool] = import_data(dataDir, files(i).name);
sp = create_figure... |
8961c4d9571415f308d126b7f6ba9e6a8759a8b5d87a97867066809226895b45 | MATLAB | 1,320 | 48 | function analysis_loop(CBF)
% List all mat files in the folder
stk_files = dir([CBF.sourceP,'*.mat']);
%% Set up file logging
diary(fullfile(CBF.folderP, sprintf('log_%s.txt',datetime("now", 'Format','dMMMy_HH-mm-ss'))))
% Initialize
fprintf('%s\n',datetime("now"));
fprintf('%s\n',version);
%% Run through all rec... |
8fad718f0557e2b23b5289c8d54ec3a8693fa32587fa7088059b85e13d2bcc3e | MATLAB | 1,320 | 60 | function TrialFcn_AMAversive_PumpControl
% TrialFcn_PumpControl(TRIALS)
%
% This function sets and controls the pump variables for the Aversive AM
% Detection task.
%
%
% Daniel.Stolzberg@gmail.com 2014. Edited by MLC 10/30/2014.
fprintf('CONNECTING TO PUMP...')
pump = serial('com1','BaudRate',19200,'DataBits',8,'St... |
0be1de3caecc37d0bf948244600b9fb0a9bc0b0a8900f8a179f869116ea30374 | MATLAB | 1,322 | 37 | function [unmixed] = main_GELMM(unmixed_FCLSU, M0, img)
% Function to unmix lambda stack based on Generalized Full Extended Linear Mixing Model (GELMM) algorithm
% -------------------------------------------------------------------------
% Inputs: unmixed_FCLSU - 6D stack of unmixed output from FCLSU
% M0 - ext... |
0242cf9720588fd24b55a71a037aec1b1305a7880dad456e2d78637396f385b0 | MATLAB | 1,323 | 37 | function plot_total_recruitment(model, args)
arguments
model (1,1) Model
args.minDiam double = -Inf
args.maxDiam double = Inf
args.quantile double = [] % Truncate threshold to this recruitment quantile
end
filterByDiam = isfinite(args.minDiam) || isfinite(args.maxDiam);
fiberActiveAll = load_ac... |
d6d79935f5bb12e78a445af8278e271c362419e44f625c8b062766bc9b9c946e | MATLAB | 1,323 | 68 | %Offline dprime calculation
%Initialize
hitrates = [];
%Pull out stimuli and response codes
Depths = [Data.AMdepth]';
Resps = [Data.ResponseCode]';
%Remove reminder trials
startInd =find(Depths ~= 1, 1,'first');
Depths = Depths(startInd:end);
Resps = Resps(startInd:end);
Stimuli = unique(Depths);
%Convert respon... |
f50276e95d456abca819e335ee0e23fb34601b294c4b717aa29e0e5f24e52eeb | MATLAB | 1,323 | 52 | classdef StructureManager
%STRUCTUREMANAGER Summary of this class goes here
% Detailed explanation goes here
properties
IDToObjTable
end
methods
function obj = StructureManager(size)
obj.IDToObjTable = containers.Map('KeyType', 'int64', 'ValueType', ... |
fab5e4eccc8e89272b6ea58abd35dded5c1c9a7518c063297d90e5382eeb9235 | MATLAB | 1,323 | 56 | function Me = Meq4e(Xe,Tz)
%***************************************************
% AeQ4E:
% Creates the element mass matrix of elastic
% quadrilateral 4-node element such that
% Syntax:
% Me = Meq4e(Xe,Ge)
% Input:
% Xe : coordinates Xe = [x1 y1; x2 y2; x3 y3; x4 y4]
% Tz : =0, z tractions assumed zero, Tz... |
40c94bfac2f2facde332b914e7e22ba8083d622949e7fb4b9013778b97b2868d | MATLAB | 1,324 | 50 | %%This function is used to check whether the fileds of MVPC are the same
%%across MVPCsets
% *** This function is part of ERPLAB Toolbox ***
% Author: Guanghui Zhang
% Center for Mind and Brain
% University of California, Davis,
% Davis, CA
% 2025 Sep
function MVPC = f_checkmvpc_str(MVPC)
if nargin <1 ... |
35da792573a364e6de6e094a55dd35ef82bdf7ba1e9244a06f3cb63a8d5e9c89 | MATLAB | 1,326 | 31 | function create_color_wheel()
% Following a solution suggested in:
% https://www.mathworks.com/matlabcentral/answers/213463-colormap-on-the-outside-of-a-circle#comment_281019
N = 256; % Number Of Colours In Colour Wheel
th = linspace(0, 2*pi, N); % Angles
... |
eee662bb8f99e44984790ca81fc3da817b65d49f276d8f282b87170fb8076d47 | MATLAB | 1,327 | 36 | function [ScoreTrain,CoeffTrain,ScoreEval,CoeffEval,explainedTrain,explainedTest] =PCAeval(X,X_)
% centre the data around zero using shared mean
mu = mean(X);
% mu = mean([X;X_]);
X = X-mu;
X_ = X_-mu;
A = (X'*X) / length(X); % compute the covariance matrix (normalised by the num of elements)
[V,latent] = e... |
81aad029c0ad3b687762527fa8fda144786ffa7b6ec6487cc4289dafa9dab028 | MATLAB | 1,329 | 47 | function handles = Remind_Callback_SanesLab(handles)
%handles = Remind_Callback_SanesLab(handles)
%
%Custom function for SanesLab epsych
%
%This function forces a reminder trial when the REMIND button is pressed
%Input:
% handles: GUI handles structure
%
%Written by ML Caras 7.27.2016
global GUI_HANDLES AX FUNCS RU... |
9f64b1604924fcdeb046d9b41505aaed5c83e13aa66db6084359d231fc38ecfc | MATLAB | 1,329 | 35 | function plotPerformance_SpatialMask_SNR
[dataDir, options, c, d] = import_settings()
% For each ferret
files = dir( fullfile(dataDir,'*.mat'));
for i = 1 : numel(files)
[COctrl, COcool, SPctrl, SPcool, SOctrl, SOcool] = import_data(dataDir, files(i).name);
sp = create_figure( fi... |
c26f7e58538827c680ae15cee19b9c38bca134e3b41f70fa6b088cb78f2e9b5d | MATLAB | 1,329 | 39 | function dOut = mahalFuncTrialWise_joon(dat1,dat2)
% calculate relative Mahalanobis of each trial between two condition
% specific centroids
% dat [trials, features, samples]
% e.g. dat = rand(150,20,500); % random data, 150 trials, 20 channels, 500 time points
% lab is a vector of binary condition values [1 or... |
c1e701e0bbc9ae5e351e294791ca0126f05f49d12e5a95de2cf3888e2d371693 | MATLAB | 1,334 | 51 | function [resultant_vr] = Dani_Function_VectorStrength (dirAng, dirAnaly, cond,cc)
%%
close all
% Load all data trials from all flies in dataset
cd(dirAng)
files = dir(['*', cond '.mat']);
NumFiles = length(files);
% Parse data by fly num, trial num
for p = 1 : NumFiles
temp = strread(char(files(p).nam... |
50842dbd1358c560e27c35baa57829a8ee7af39d888caa5644b4dd8fbdfa1e17 | MATLAB | 1,335 | 27 | % TPPREVIEWIMAGEFUNCTIONLISTGLOBALS - Declare global variables for TPPreviewImage functions
%
% Declares the global variable
%
% TPPreviewImageFunctionList -- a structure list of installed TPPreviewImage functions
% TPPreviewImageFunctionChannelList - a list of installed acquisition channels, such
% ... |
e0eaad5911986533600c29218ff54d6f2dae29cc3bcdc58fbbf838fa9118b17c | MATLAB | 1,335 | 22 | % FILTER TRIALS BASED ON DISTRIBUTION CUTOFFS %
function [filtered_combined_data, filtered_combined_data_cutoff_logical] = bst_ast_distribution_filter(max_amp_range_all_trials, trialAmpHighCutoff, ...
max_grad_range_all_trials, trialGradHighCutoff, all_amp_data_bad_chnls_removed)
% Take out any trials with... |
17cf718f0e1372a96c21f0710d5f66105b3d0abef202a89f448a2a4bf72529d8 | MATLAB | 1,338 | 37 | function [LP,D]=LinearPattern(X)
% function Y=LinearPattern(X,type) output column and row means from all 4 subsignals, subsampling by 2.
% X 2-D matrix
% LP.r11, LP.r12, LP.r21, LP.r22 are row means (column vector)
% LP.c11, LP.c12, LP.c21, LP.c22 are column means (row vector)
% D The difference between... |
522441a35cb3b27363ee6bc9cef33d3847ffbfe8332bc0911d5b26c28176bcf4 | MATLAB | 1,340 | 56 | function [MD,FA,eigVals,DT] = estDT(sigVals, bVals, bVecs)
%
% Estimate diffusion tensory
%
% sigVals: [N_bval * Nx * Ny * Nz] matrix
% bVals: [N_bval * 1] vector [s/mm^2]
% bVecs: [N_bval * 3] matrix [s/mm^2]
%
% (c) 2022, Corey Baron
% Check inputs
szin = [size(sigVals), 1];
if ~isreal(sigVa... |
82d217bf72da86871b0263d7b241aa1fc5539f0185d156e7f32b0b0e5aee54ff | MATLAB | 1,340 | 59 | %quick and dirty tool for plotting out HMC sample progress
% I didn't document this well, but it's not super imporant
% This prints out stuff I want for the DMC task GMLM, but not every GMLM
function [] = plotSamples(obj, samples, sample)
clf;
TotalSamples = size(samples.H, 2);
if(nargin < 3 || isempty(sample))
sa... |
dd460918b260ccee419a5c0e1bd7d3ef79fdf06682e17dbf266b22ae63a5651b | MATLAB | 1,342 | 31 |
function PTParameters=initialize_psychToolbox()
Screen('Preference','SkipSyncTests',1);
KbName('UnifyKeyNames');
AssertOpenGL;
KbCheck;
WaitSecs(0.1);%wait 0.1 secs
GetSecs;
sound(1); %initialize sound so that doesn't take too long first time we use it
presentation_screen = max(S... |
8f525cfb967f049da9a9796e883afee099bf95d9cc36ae3e2090516e8ca6b471 | MATLAB | 1,343 | 43 | % demo use script
suite2p_exper_dir = ['/Volumes/van-hooser-lab/Users/Diane/For_Steve/SCN1-722'];
target_directory = ['/Users/vanhoosr/Desktop/2722-05-05'];
directory_mapping{1}{1} = 't00001-001';
directory_mapping{1}{2} = {'t00001-001'};
directory_mapping{2}{1} = 't00002-001';
directory_mapping{2}{2} = {'t00002-0... |
76f2ea797c6dfc412092b47e1b4643c0bc2501f0787b21e4dbba5557a85bd6ce | MATLAB | 1,345 | 35 | function str_out = get_str_param(struct_param)
% Based on input parameters (as given by function get_all_params_to_test),
% return a string describing the model parameters.
%
% struct_param = struct('AboutFirst','WithoutFirst', 'learned_param', 'transition',...
% 'decay',[Inf],'decayF', [Inf], 'window', [Inf],... |
5d53cd7634422ac4f02038e255d3cd69639ad25401e5f61c507bba7ff1fcd26d | MATLAB | 1,347 | 55 | % mvpch - history function for MVPCsets.
%Author: Guanghui ZHANG
%Center for Mind and Brain
%University of California, Davis
%Davis, CA, USA
%2024
function str = mvpch( command);
str = '';
if nargin<1
help mvpch
return
end
if isempty( command )
return;
end
try ALLMVPCCOM = evalin('base','ALLMVPCCOM');c... |
0f7d4daa06d93f6597101b7fd45816153125f5d685b62bf9e76ec9fdf7999877 | MATLAB | 1,349 | 64 | function M = lta_read(fname)
% M = lta_read(fname)
%
% lta_read.m
%
% Original Author: Bruce Fischl
% CVS Revision Info:
% $Author: greve $
% $Date: 2014/07/10 04:11:44 $
% $Revision: 1.5 $
%
% Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
%
% Terms and conditions for use, reproduction... |
e2e0b923c422b4225b07c8719ff92000614a6643d9eb7c23b73ed111c661f782 | MATLAB | 1,350 | 29 | function fiberCenter = shift_inside(fiberCenter, area, buffer)
% Tested to work with multiple regions and holes
% Shift fiberCenter towards the closest edge of 'area'
% buffer can be the fiber radius for example or radius plus min distance
[d, x_poly, y_poly] = p_poly_dist(fiberCenter(1), fiberCenter(2), area.Verti... |
c6d46031d0a61f72a8422261c21dad02230cedd1705d1fc67999570d864052e1 | MATLAB | 1,352 | 40 | function wsws_ICA_plot(snum, file)
% function to plot IC topographies and timeseries
% snum = subject number (scalar)
% file = 'train' or 'test' data
run(['..', filesep, 'def_local'])
addpath(path_fieldtrip)
ft_defaults
% load hdr & comp struct
if strcmp(file, 'train')
fprintf('... loading training components fro... |
564fe870d8449f98c7538c6d9e1c77f8b6cd7462bc57002936f27e040ff7f9aa | MATLAB | 1,353 | 43 | function feedback(correct, side)
global DA gf
gf.TrialNumber = gf.TrialNumber + 1;
if correct == 1,
if side == 0,
valve(4,200,1,5,'left') %(bit, pulse_time, pulse_N, index and name for recording time)
elseif side == 1,
valve(5,200,1,7,'right') %(bit, pulse_time, puls... |
a7985e8141d901a729c7d47e696da14e2cd02b0e94054d12d5e87060d906914b | MATLAB | 1,355 | 37 | %% Setup
% This script combines sessions from different tastes to make a combined
% connectivity matrix between the hemispheres
util.clearAll;
% stimuli
outdir = fullfile(util.get_paths().figs,'compare_tastes_corr');
util.mkdir(outdir)
%% load the data and combine betas
% Get the beta tables from matfiles
taste_str = ... |
6eadeb51f2dbd59deeaa40be26dc14b8b545f715cc5b703c71bdaa253ed266fe | MATLAB | 1,358 | 39 | function main_figure(unmixed, M0, lambda, channel, filename)
% Function to generate and save figures
% -------------------------------------------------------------------------
% Inputs: unmixed - 6D stack of unmixed image
% M0 - extracted fingerprints
% lambda - array of lambda (wavelength) values of m... |
6c3b6307516f9773a785c866eddc0c94a702a8530a47af6b2e97a8c83eba7379 | MATLAB | 1,360 | 48 | clear
datafile = 'IMDBMULTI';
load(sprintf('%s/%s.mat', datafile, datafile));
label = label - min(label);
fid = fopen(sprintf('%s/%s.txt', datafile, datafile), 'w');
fprintf(fid, '%d\n', length(label));
for i = 1 : length(label)
g = graph_struct(i);
num_nodes = length(g.al);
fprintf(fid, '%d %d\n', num_n... |
3642aa91035f932040f815071bdcdeb528a31d0ec6fac55237fbd15217dd8ef7 | MATLAB | 1,361 | 54 | function [detvtx,pth] = SStat_mass_FDR2(pval,maskvtx,rate)
% [detvtx,pth] = SStat_mass_FDR2(pval,maskvtx,rate)
%
% Two-stage FDR approach to achieve tighter control of the FDR. This
% procedure is more powerful than the original FDR procedure implemented in
% SStat_mass_FDR.
%
% Input
% pval: P-values.
% maskvtx: Mask'... |
54eca5e5b27fc591cb2851096c9374dec30c369663883a143883e159c19abe93 | MATLAB | 1,363 | 63 | function varargout = PumpControl_SanesLab
% pump = PumpControl_SanesLab
%
% Custom function for SanesLab epsych
%
% This function sets and controls a New Era-1000 Syringe Pump.
%
% Outputs:
% varargout{1}: serial port object associated with pump
%
%
% Daniel.Stolzberg@gmail.com 2014. Edited by MLC 4/5/17.
%Close a... |
7dbd3eb6d8621c2fc5a1cea09d3295d7ae921ff4beb05f28673d9b92abefe23b | MATLAB | 1,363 | 57 | function spikes = pp_sort_channel(data, thresh, reject)
%
% spks = pp_sort_channel(data, thresh, reject)
% Runs the UMS algorithm for data of a given channel/group of channels.
% Important: include the optional inputs to ss_default_params, in order
% to use the thresholds calculated from clean data segments.
... |
a00cf9384928c904e33440a5dd9604275eb490f922404bc8b641dcd2fbe08fd1 | MATLAB | 1,364 | 46 | function padded = padmatrix(input, wherepad, padval)
% UltraMegaSort2000 by Hill DN, Mehta SB, & Kleinfeld D - 07/09/2010
%
% padmatrix -- pad a matrix
%
% Usage:
% padded = padmatrix(input, wherepad, padval)
%
% Description:
% PADDED = PADMATRIX(INPUT, WHEREPAD) adds zero rows/columns to the
% matrix INPUT. W... |
5959381ad2ee39f0df05fdc8e991879e3f8318a77bc350cf2c83d7d4ee47f3b6 | MATLAB | 1,365 | 51 | %% GIFT ICA to Slicer colormap
Pma = 'H:\DataProcessing\GIFT_\ALL_mean_component_ica_s_all_.nii';
Patlas = 'D:\ownCloud\PROJECTS\MRI\FINALIZED\SlicerFinal8\CorticalAtlas-Split.nii';
Tareas = 'D:\ownCloud\PROJECTS\MRI\FINALIZED\conn_catlas.txt';
Tcolors = 'D:\ownCloud\PROJECTS\MRI\FINALIZED\CATLAS_COLORS-SPLIT.txt';
th... |
e4887d3a0e30c21d1dba2f68dc9e5d73f94b98dfb03df836b73cc15340c24c69 | MATLAB | 1,365 | 48 | function E = DB_GetElectrode(tank_id)
% E = DB_GetElectrode(tank_id)
%
% Returns electrode info for a tank with database index 'tank_id'
%
% All depths are in microns
%
% Daniel.Stolzberg@gmai.com 2014
try
E = mym([...
'SELECT e.target,e.depth,e.tank_id, ', ...
't.manufacturer,t.pi... |
8f58d19d77a3e88231c8f388641e5611e13b62db80803cb83e2428f79b8073d1 | MATLAB | 1,366 | 36 | function colors = emphasize_cluster_colors(spikes)
% UltraMegaSort2000 by Hill DN, Mehta SB, & Kleinfeld D - 07/12/2010
%
% emphasize_cluster_colors - make color matrix for each minicluster ID
% where the colors for clusters are separated
%
% Usage:
% colors = emphasize_cluster_colors... |
afa422296e07d237ec9d47c8e1633b1509076ef86868f61811b522b44e3b152f | MATLAB | 1,367 | 38 | function totalThresh = compute_total_thresh(model, threshMode, threshValue)
%COMPUTE_FASC_THRESH Calculate recruitment threshold of fascicles
% Default (w/ only one argument passed) is 10% recruitment
% fascThresh iAS x iFasc
% Inf means missing value (i.e. out of active site range)
% NaN means out of inje... |
07b2482d2ee8e8ca7657059b1122edec22b617d9fdd258e5e76f7f918476a8c5 | MATLAB | 1,369 | 23 | %-----------------------------------------------------------------------
% Job saved on 08-May-2022 10:00:51 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
clear matlabbatch
subjfolder = dir('F:\fMRI_QC\fm... |
b1132d55884f91bae853f7cb17a184f7cb7a545e9dca2be5460093658f994114 | MATLAB | 1,370 | 55 | function e = UpdateDAtags(DA,TRIALS)
% e = UpdateDAtags(DA,TRIALS)
%
% DA is a handle (or array of handles) to the OpenDeveloper ActiveX control
% returned from a calls to SetupDAexp.
%
%
% TRIALS.NextIndex is the trial index which will be used to update parameter tags
% running on RPvds circuits
%
%
% ... |
e1436f69a597aa426c50fdb3ad74dc4ea44c4f2b3394be7c8c955205d182c7e3 | MATLAB | 1,373 | 24 | function [super_noise] = expectation_conditioned_on_constituent_parts_2D(actual, raster,neuron_window, time_window)
[expected,unscaled_expected, p] = theoretical_expectation_2D(raster, neuron_window, time_window)
super_noise = [
expected(1),
expected(2),
(e... |
137362edea8b67f1d2e117c1cd3936fbb27fa35214b054955b11887f9c76b0d4 | MATLAB | 1,374 | 48 | function [class_contribution] = triple_correlation_class_contributions_3D_sp_wr(arr, x_window,y_window, time_window)
class_contribution = zeros(1,14);
class_count = zeros(1,14);
max_time_lag = ceil(time_window / 2);
[N_x, N_y, N_times] = size(arr);
for x1 = -floor((x_window / 2)):ceil((x_... |
6635b35a96746cf0e988af9c3049d3bf6e7a3b24b62cee82d67e4723a0d146f7 | MATLAB | 1,374 | 37 | function analyzetpstack_correctdriftall(fignum, channel)
ud = get(fignum,'userdata');
ds = dirstruct(getpathname(ud.ds));
answ= {'[-6:2:6]','[-6:2:6]','[-100:10:100]','[-100:10:100]','10','5','1','1','0'};
searchx = eval(answ{1}); searchy = eval(answ{2}); refsearchx = eval(answ{3}); refsearchy = eval(answ{4});
howof... |
c1ee2239b7dd18a7ede18b88029028ddb5da03e09d4e65b2f031260338ca9456 | MATLAB | 1,374 | 36 | function fiberCompartMod = assign_mod(fibersCompart, motoR)
%% count fibers in nerve
% get ids of non-empty fascicles TODO: only assign to fibers reached by AS?
fascIdsNonEmpty = find(~cellfun(@isempty, fibersCompart));
% loop non-empty fascicles to sum up fiber numbers of all populations
nFibsTot = sum(cellfun(... |
9658221d414bc77220d54b3bb44c504720304c0fb37998a5a70b5481b57477f1 | MATLAB | 1,376 | 22 | %-----------------------------------------------------------------------
% Job saved on 17-Jun-2022 09:26:13 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
clear matlab
subjfolder = dir('F:\fMRI_QC\fmri-op... |
3d69ea8e3b703a4b4a6b92d4592d18b570ac340840f305b328a6af9ac052e138 | MATLAB | 1,377 | 22 | %-----------------------------------------------------------------------
% Job saved on 17-Jun-2022 09:26:13 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
clear matlab
subjfolder = dir('F:\fMRI_QC\fmri-op... |
bc30ce40216c67d3c98934dd6ea15bb9e15f16222eab09d90e738d79303ffad6 | MATLAB | 1,378 | 39 | function [unmixed] = main_ELMM(unmixed_FCLSU, M0, img)
% Function to unmix lambda stack based on Full Extended Linear Mixing Model (ELMM) algorithm
% -------------------------------------------------------------------------
% Inputs: unmixed_FCLSU - 6D stack of unmixed output from FCLSU
% M0 - extracted fingerp... |
f197b11214076ff2da8aa3d3cf31b5a2879f5c6432a08cf997576471e5b93455 | MATLAB | 1,380 | 50 | function [data] = linear_regression_data_generator(n, d, std)
% Data generator for linear regression problem.
%
% Inputs:
% n number of samples.
% d number of dimensions.
% std standard deviation.
% Output:
% data data set
% data.x_train ... |
f9fd0369904f0a7a87fa8884480f360e9938f388e94ab8fa22b2eef2ce2f53ae | MATLAB | 1,382 | 38 | function [recrNormIa, recrNormIb, recrNormAlpha, recrNormII, ...
recrNormIII, recrNormTouch, Q] = upsample_recr(recrNormIa, ...
recrNormIb, recrNormAlpha, recrNormII, recrNormIII, recrNormTouch, Q)
%UPSAMPLE_RECR Summary of this function goes here
% Detailed explanation goes here
factor = 10;
if facto... |
37c9f775c8177be72f6303113932706f679be2c7bd4ea2e030bd7d85ba221305 | MATLAB | 1,383 | 46 | function [sigma_noisy] = spike_to_calcium(sigma_sim, params, flnoise)
% function [sigma_noisy] = spike_to_calcium(sigma_sim, params, flnoise)
%
% Transfers spiking data to calcium transients, convoluting the spikes
% with exponential decays.
%
% Input: 1. sigma_sim: N * T matrix, with 0 and 1's giving spikes
... |
39bc0a8185e592d19d41c9b256953d924897b4aadc4bfe6cbdc8ab7da3176b68 | MATLAB | 1,383 | 52 | function CSD = CSD_construction(lfp,z,plt,tt)
%%% Adapted from https://github.com/haiderlab/Current-Source-Density
%% estimate CSD
% 5 point hamming filter from Ulbert et al. J Neurosci Methoods 2001
% ('Multiple microelectrode-recording system for intracortical
% applications') - equation 5 for sp... |
7006f3032f771c3cdb80abcef1d545e69040a3d1503144d66118e5d6bd943615 | MATLAB | 1,384 | 41 | function fascThresh = compute_fasc_thresh(modelOrFiberThresh, threshMode, threshValue)
%COMPUTE_FASC_THRESH Calculate recruitment threshold of fascicles
% Default (w/ only one argument passed) is 10% recruitment
% fascThresh iAS x iFasc
% Inf means missing value (i.e. out of active site range)
% NaN means ... |
1fb5b41f2f7952713aa9019683b78d76bf9e368142022fd0f31d0f36e4347091 | MATLAB | 1,389 | 40 | function activeArray = makeActivePatternsArray(patterns, npat, nt)
%MAKEACTIVEPATTERNSARRAY converts pattern matrix to activity array
% This function takes the PATTERNS matrix output by FINDALLPATTERNS and
% converts to a PxT matrix giving the number of patterns of each time
% present at each time step, where P i... |
4a6310f1e24a2448a33f3eedc7d1287476ab9e2fc8199a3896b37bdafb5011c7 | MATLAB | 1,389 | 44 | function [im,params]= previewprairieview(dirname, numFrames, firstFrames, channel)
% PREVIEWPRAIRIEVIEW - Preview PrairieView image data
%
% IM = PREVIEWPRAIRIEVIEW(DIRNAME, NUMFRAMES, FIRSTFRAMES,CHANNEL)
%
% Read a few frames to create a preview image. DIRNAME is the
% directory name to be opened, and NUMFRAM... |
99329348a2f2b6a1743d634bf3bd12767acb1d99fc7ce03c9819fe0b19602a29 | MATLAB | 1,390 | 65 | function [log_stds, d_log_scales] = scaledGaussianComponent(ws, log_scales_0, grps, dU_0, log_stds)
% i.i.d. multivariate zero-mean normal prior distribution over columns of ws with covariance matrix
% defined in GMLMprior_dmcStimVar
%
% calculates prior and all derivatives
compute_D1 = nargout > 1;
precomputed... |
078508b0cf50ab009936ed47bb33eacb734b757f543c3b7d0a3569d7c9091b29 | MATLAB | 1,392 | 24 | function [super_noise] = expectation_conditioned_on_constituent_parts_3D(actual, raster,x_window, y_window, time_window)
[expected,unscaled_expected, p] = theoretical_spiking_expectation_3D(raster, x_window, y_window, time_window);
super_noise = [
expected(1),
expected(2... |
19288781f74b38a26f24bd8a126af66286114f80df1b7994c18a0bf25d700b71 | MATLAB | 1,392 | 41 | function y = istrue(x)
% ISTRUE converts an input argument like "yes/no", "true/false" or "on/off" into a
% boolean. If the input is boolean, then it will remain like that.
% Copyright (C) 2009-2012, Robert Oostenveld
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and ... |
4038b26fb80f0745f13b2fd44e4bf8f108695489751dca4f5fd8be44af1e9e9a | MATLAB | 1,392 | 55 | function data = ft_read_lfp_tdt(tank,block)
% data = ft_read_lfp_tdt(tank,block)
%
% Read continuous (LFP) data from TDT Tank and convert for use with
% FieldTrip toolbox
%
% See also, trialfun_tdt
%
% DJS 2013
if nargin == 0 || isempty(tank), tank = char(TDT_TankSelect); end
cfg.tank = tank;
cfg.datatype = 'Blo... |
f66e1efbc1d3a67fa40c348a2b6793d6a2e08374e9318067c5a3c28d92868d3b | MATLAB | 1,393 | 58 | function [Rcorr,nRcorr] = SchreiberCorr(S)
% Rcorr = SchreiberCorr(S)
% [Rcorr,nRcorr] = SchreiberCorr(S)
%
% Implements spike-train reliability measure introduced by Schreiber et al,
% 2003. An Rcorr approaching 1 indicates very high spike-time reliability
% across trials, whereas Rcorr approaching 0 indicates very p... |
bf6c158edc52e9bcf135dc1d54fda9b10fa92c39df3c774c7287f8c1bcd49d86 | MATLAB | 1,396 | 65 | %% Simple Whole-Screen Flash
%
% Daniel.Stolzberg@gmail.com 2016
% Modifiable Parameters
FlashDur = [0.5]; % flash duration (seconds)
ITI = [2 5]; % inter-trigger interval (seconds)
FlashOnColor = 1; % flash intensity [0 1]
FlashOffColor = 0; % flash intensity [0 1]
NFlashes = 100; % number o... |
e5f831270b66ccbd74a223073b4536deba561fc93fee0b7e9fa1afc22c837d83 | MATLAB | 1,396 | 39 |
p=8; % selecting the participant
Indcs= IL_Inds{p}; %Get the indices for various trials of an specific Surface-Foot combination
data= IL_inputs; %Get the indices for various trials of an specific Surface-Foot combination
tit={"Participant 8", "Left Foot - Sloped Surface"} ; % set the title of plot
... |
b44bde773f1bad6bde5b57c317de66459871bc31f03c7e7154101d3849035d6c | MATLAB | 1,397 | 40 | function [ Node ] = ColladaAddStandardAccessor( DOM, Node, ArrayName, Count)
%COLLADAADDSTANDARDACCESSOR( DOM, Node, ArrayName, Count)
%Create a standard accessor for verticies and normals, i.e:
%<technique_common>
% <accessor count="8" offset="0" source="#box-lib-positions-array" stride="3">
% <param name="X" ... |
191df73b45efa62544515ff29890c23eaf1dfab2851dd609df421cdb7d6b02c5 | MATLAB | 1,398 | 51 | function [] = reduce_hspace_subplot(h_subplots, percent_removed, increase_width)
% Reduce the horizontal space between subplots by percent_emoved percents.
if nargin<3
increase_width = 1 ; % otherwise, shift towards center
end
pos = get(h_subplots,'position') ;
n_subplots = length(pos) ;
right1 = pos... |
1baf88a517cfa13da7e8ca3814cd50fdcc0e5cd0dcb9478c0c5bc5940229f412 | MATLAB | 1,399 | 46 | function [im,params]= previewprairieview(dirname, numFrames, firstFrames, channel)
% PREVIEWPRAIRIEVIEW - Preview PrairieView image data
%
% IM = PREVIEWPRAIRIEVIEW(DIRNAME, NUMFRAMES, FIRSTFRAMES,CHANNEL)
%
% Read a few frames to create a preview image. DIRNAME is the
% directory name to be opened, and NUMFRAM... |
24399baaf5a737cee0721e37f8d3b6ffea8c157434e74a1ba851b4da66dbc797 | MATLAB | 1,399 | 56 | %=========================================================
% FileName: linear_classifier_test.m
% Designby: Zhe
% Modified: 09/02/2021
% Describe: Testing linear classifier for the position decoding
% from FPGA recorded traces.
%=========================================================================
clear... |
86429685cc7e505c99a5a2c7ae7813c2126823b18202153b552bf3c147accf9a | MATLAB | 1,399 | 45 | function im = tppreview(dirname, numFrames, firstFrames, channel)
% TPPREVIEW - Preview twophoton image data
%
% IM = TPPREVIEW(DIRNAME, NUMFRAMES, FIRSTFRAMES,CHANNEL)
%
% Read a few frames to create a preview image. DIRNAME is the
% directory name to be opened, and NUMFRAMES is the number of
% frames to read.... |
eb33df2156c16d74cf103c055688d42ece66d5d1b5319c9bcf20962354b3f56e | MATLAB | 1,399 | 46 | function P = slice_AS(model, project, planeP, planeV, roundPrec, iActiveSites)
arguments
model (1,1) Model
project (1,1) logical
planeP (1, :) = [] % Default is centered at each AS z. Point in plane, if given scalar it is auto-broadcasted to vector
planeV (1, 3) = [0, 0, 1] % Vector perpendicular ... |
b4fc20b5dae26e77fd9ca941012abf149cb3f364eb533557185f52da5e0a037b | MATLAB | 1,400 | 40 | % Loads and plots factor loading (assembly membership of units into assemblies during each experimental phase
%
% Aleksander PF Domanski PhD UoB 2015
% aleks.domanski@bristol.ac.uk
%
% NB assumes factors have been calculated on each area independently, thus
% units may not line up based on exlusion criteria not b... |
8056ee4d3c2699f134eb15cf3530eab82ca78f4346df86451fde30f78a1eb4cd | MATLAB | 1,401 | 45 | bDir = '..\data\';
dirList = {'1. ABJ','2. JHS(x)', '3. JJH', '4. KCH', '5. SYS(x)', '6. KDH','7. OSL(x)','8. KSH', '11. LJJ(x)', '12. SHH(x)', '13. SJH', '15. SSK', '16. BSW', '17. KKM'};
GoodChannel = [2 3 30 6 7 28 29 8 24 25 34 35 62 37 36 63 60 39 58 41 40 57 56 11 12 23 22 15 14 13 19 20 16 17 18 43 53 54 ... |
00b89ac54ae19bb7a0130bd5c5708dd9b8a4b5494c3817d53bd8ec1f9ac8f175 | MATLAB | 1,402 | 64 | function fit1 = fitness_moea20(A1, paramsvec, eegdata1, paramstoest, T1,tcut, fhz1)
paramsinput = [paramsvec, zeros(1,10)];
paramsinput(paramstoest) = A1;
% load in the data to fit against
eegautocor = eegdata1{2};
eegdatadegdist = eegdata1{5};
a2=[];
fithvg=[];
parfor RunIter = 1:5 % run 5 times for stabil... |
7d4c33477c5dcff70d463b70d4c265df61b457300b04e61d3e88b62e840c8342 | MATLAB | 1,403 | 52 | function D = CalculateFlowMatrix(prevFrame, currFrame)
if length(size(currFrame)) == 2
I0 = im2double(prevFrame);
I1 = im2double(currFrame);
else
I0 = im2double(rgb2gray(prevFrame));
I1 = im2double(rgb2gray(currFrame));
end
I0 = single((I0-min(I0(:))) ./ (max(I0(:)) - min(I0(:))));
I1 = single((I1-min... |
a39888c8b1062f49dd7d7fcb4b434000ac9266092151a1d69a3c3f7bb2876ccd | MATLAB | 1,403 | 47 | function im = tppreview(dirname, numFrames, firstFrames, channel)
% TPPREVIEW - Preview twophoton image data
%
% IM = TPPREVIEW(DIRNAME, NUMFRAMES, FIRSTFRAMES,CHANNEL)
%
% Read a few frames to create a preview image. DIRNAME is the
% directory name to be opened, and NUMFRAMES is the number of
% frames to read.... |
5609ceced0614b973b94571f07f222868fd1e5f42aa8a09853bf3220cc60e321 | MATLAB | 1,404 | 51 | function [data] = multiclass_data_generator(n, d, l, std)
% Data generator for multiclass classifier problem.
%
% Inputs:
% n number of samples per class.
% d number of dimensions.
% l number of classes.
% std standard devision of gaussian pr... |
23b77c262e3d57dab56b2a4e0fc71cf501822c1e7f955fa5177537402f740334 | MATLAB | 1,406 | 43 | function ExtractFeatures(self, varargin)
%EXTRACTFEATURES Extracts spatial/temporal features from project frames
% EXTRACTFEATURES(SELF) extracts features from streams and cameras
% specified by STREAMS and CAMERANAMES in config.txt
%
% EXTRACTFEATURES(..., 'PARALLELIZE', TRUE) parallelizes process (by
% defa... |
88db8693344dc44685edab6ab7b2a05de6cd58e1bbf56fad623076e9f3a94859 | MATLAB | 1,408 | 45 | % PURPOSE: gets current ERPLAB's version
%
% FORMAT:
%
% version = geterplabversion;
%
% or
%
%
% [version reldate] = geterplabversion; % reldate=release date
%
%
% *** This function is part of ERPLAB Toolbox ***
% Author: Javier Lopez-Calderon
% Center for Mind and Brain
% University of California, Davis,
% Davis, ... |
7e6a80338cc31ebd21f3b96cc0dbd8d82531e7715f99f4c0851bc390828282c8 | MATLAB | 1,411 | 77 | %% Flip Checkerboards
% Sends 1 ms pulse from from Bits# TrigOut to TDT digital input on every
% Checkerboard flip.
%
% DJS 3/2016
nFlips = 100; % # flips
IFI = 1; % inter-flip interval (seconds)
nCheckers = 10;
[window,ScreenRect,frameRate] = PTB_NormalExpt_Startup(0,1);
black = BlackIndex(window);
white = WhiteIn... |
6bee79641dd31ccad6e0362077fdaa9b0a60853984d23e8050841b544a6853c6 | MATLAB | 1,412 | 40 | function [umo,vmo,p11,p12,p21,p22] = tvl1_optimization(um,vm,grad,rho_c,Iw1x,Iw1y,p11,p12,p21,p22)
epsilon = 1e-2;
OUT_ITERATION = 10;
INNER_ITERATION = 30;
tau = 0.25;
[M,N] = size(vm);
sz = M*N;
theta = 0.1;
lambda =50;
taut = tau / theta;
n_inter=0;n_outer=0;error = 1000000;
... |
72456209d48ae4a08ee71a67e80d42bffea844019fce8857c84e8ea58627a6de | MATLAB | 1,412 | 60 | % PURPOSE: subroutine for ploterpGUI.m
% Creates default Y ticks for ERPLAB's plotting GUI
%
% FORMAT
%
% [def miny maxy] = default_amp_ticks(ALLMVPC, yrange)
%
% INPUTS
%
% ALLMVPC - ALLMVPCset
% yrange - min and max ALLMVPC amplitudes
%
% OUTPUT
%
% def - tick values to show in Y axis
% miny ... |
84e498322497e9740fd6d4db5957a48fe644fb1eb46adbc2b6d9e88dfa9e9e9c | MATLAB | 1,413 | 49 | function handles = findModuleIndex_SanesLab(moduletype, handles)
%handles = findModuleIndex_SanesLab(moduletype, handles)
%
%Custom function for SanesLab epsych
%
%Inputs:
% moduletype: a string containing the desired TDT device
% handles: GUI handles structure
%
%Example usage: handles = findModuleIndex_SanesLab('... |
1817a97fa47adbf35510ca6fe41c879bddef835322447bfcc931920b0c7e0537 | MATLAB | 1,414 | 55 | function v = dist_var(val, pgrid, doWarning)
% Compute the variance (v) of a probability distribution (val) over a discrete
% grid (pgrid).
%
% Usage:
% v = dist_var(val, pgrid, doWarning)
% NB: doWarning: 1 allow a warning message on whether the distribution is
% normalized to sum to 1 (default: 0)
%
% Copyright ... |
5cecec7431a928d2addab8d467dbf4716018c07881e328e25726f76e01f348ca | MATLAB | 1,414 | 75 | % function fcn_gnets(
clear all
close all
clc
k = 5;
params = rand(k*(k - 1),1)*10;
N = 128;
sz = rand(k,1);
sz = sz/sum(sz);
sz = round(sz*N);
while sum(sz) ~= N
dff = sum(sz) - N;
if dff > 0
for i = 1:dff
r = randi(k);
if sz(r) > 0
sz(randi(k)) = sz(randi(k)) -... |
837da3d902be9de66ff9063bb6a632d2c60ee30220ce51c160ec0034878225ef | MATLAB | 1,416 | 58 | function [rho pval] = circ_corrcl(alpha, x)
%
% [rho pval ts] = circ_corrcc(alpha, x)
% Correlation coefficient between one circular and one or more linear random
% variables (1 column per variable).
%
% Input:
% alpha sample of angles in radians
% x sample of linear random variable
%
% ... |
6e99114f999472993192e8c8f8c830c6c4890d91338dd9d857c95345f44f52d4 | MATLAB | 1,417 | 52 | function previews2tif(ds, dirname,scale,map)
% PREVIEWS2TIF - Convert all preview images in a 2P directory to TIF
%
% PREVIEWS2TIF(DS, DIRNAME [, SCALE, MAP])
%
% DS is a directory structure DIRSTRUCT object.
%
% The files will be written in the DIRNAME/analysis/scratch directory.
%
% All files will be scaled by t... |
40836bb0fc1b601ede3e0cab62c6576a360ed49deb3d9b08e0e6ebeac4b0d343 | MATLAB | 1,418 | 40 | % *** This function is part of ERPLAB Toolbox ***
% Author: Javier Lopez-Calderon
% Center for Mind and Brain
% University of California, Davis,
% Davis, CA
% 2009
%b8d3721ed219e65100184c6b95db209bb8d3721ed219e65100184c6b95db209b
%
% ERPLAB Toolbox
% Copyright © 2007 The Regents of the University of California
% Creat... |
2d4d7da0db5e5ed9b772bf16d45ee8e9ae7226651e4c3a5553c9bb8af696d4b4 | MATLAB | 1,422 | 38 | function model = load_model(subject, electrode, as, loadPotentials)
%LOAD_MODEL Summary of this function goes here
% Detailed explanation goes here
if nargin < 4
loadPotentials = false;
end
modelName = [subject '_' electrode];
modelNameAS = [modelName '_AS' as];
load(['data\Nerve\' subject '_noElectrode\Epineu... |
7f94dc94e52300852e5e47ef5aaae351ac01f84b7391a57d70d120e4368fcba8 | MATLAB | 1,425 | 52 | function [b b0] = circ_skewness(alpha, w, dim)
% [b b0] = circ_skewness(alpha,w,dim)
% Calculates a measure of angular skewness.
%
% Input:
% alpha sample of angles
% [w weightings in case of binned angle data]
% [dim statistic computed along this dimension, 1]
%
% If dim ... |
84d412b6fc5f646f7a32c26daf8325264133c6c5ce17ec7cadc9bc0a64c4cf5c | MATLAB | 1,428 | 47 | % function for finding and saving spike times for columbia data set
% Arguments: file_id = patientID + recording number
function fx_find_spikes_columbia_data(file_id)
% Load corresponding mua file
mua_file = [file_id, '_mua.mat'];
load(mua_file, 'data', 'metadata')
% run status update
dateti... |
2dc6c512ee21c2a4927646fd992ad2db4b7a75fe21153eda95b7a94fd21a0a85 | MATLAB | 1,429 | 51 | % X: data matrix, each row is one observation, each column is one feature
% d: reduced dimension
% type: type of kernel, can be 'simple', 'poly', or 'gaussian'
% para: parameter for computing the 'poly' and 'gaussian' kernel,
% for 'simple' it will be ignored
% Y: dimensionanlity-reduced data
% ... |
4d1296adf88b8735143b83ee636c6ccfaeb7f909220b54668050af469489a1f3 | MATLAB | 1,429 | 51 | function pw = lme_realizedPower(stats,C,alpha)
% pw = lme_realizedPower(stats,C,alpha)
%
% Power associated with a contrast C for the actual realization of the
% linear mixed-effects model (Depends on the Statistics toolbox).
%
% Input
% stats: Struc... |
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