sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b762731c0cc21292dea1b906893a65408fb69e78108de9941e508777c095fea9 | MATLAB | 3,459 | 117 | function [D0,phisq0,st] = lme_fit_EMinit(X,Zcols,y,ni,e)
% [phisq0,D0,st] = lme_fit_EMinit(X,Zcols,y,ni,e)
%
% Starting values for linear mixed-effects estimation.This function is
% intended to be used to provide starting values for the lme_fit_NR and
% lme_fit_FS functions by mean of some initial iterations of the
... |
78ee124b3566215ad65130cc5b33d7724c752542d1a9c0ddf6c64a1d4636efdb | MATLAB | 3,460 | 125 | function createAnisotropicFibrosisProblem(filename, fibrosis_density, mesh_spacing, orientation)
% This function creates tissue of a single consistent property, then fills
% it with fibrotic occlusions of the requested density. The fibrotic
% occlusions are arranged as barriers oriented either vertically or
% horizonta... |
cc72dedc8025b4e2caae71292627ab8829017439796f28802df35a54827a6c2d | MATLAB | 3,461 | 99 | function [wave, pattType] = generatePattern(gridSize, pattType, amp, ...
freq, wavelength, loc, vel, gausswidth)
% GENERATEPATTERN generates a custom wave pattern based on inputs
% INPUTS:
% - gridSize: 3 element vector [NX NY NT] giving the x, y, and time
% dimensions of the grid underlying the wave patter... |
e725b34974bf05e708a7e9b2c8f5c55835019681f63e909143044626fbbd31b8 | MATLAB | 3,464 | 99 | function [rowcoords, colcoords, patType, jacobians] = classifyCrit(vx, vy, edgeDistance)
% CLASSIFYCRIT finds and classifies the critical points in the vector field
% defined by VX and VY. Outputs 2 1xN vectors (where N is the number of
% critical points detected) expressing the row and column coordinates of
% e... |
80433877ac56c5ae39efadc9aac74f8d104148d7535b57d0b0d41f425bcf9542 | MATLAB | 3,465 | 92 | % axcopy() - Copy a Matlab figure axis and its graphic objects to a new pop-up window
% using the left mouse button.
%
% Usage: >> axcopy
% >> axcopy(fig)
% >> axcopy('noticks')
% >> axcopy(fig, command)
%
% Notes:
% 1) Clicking the left mouse button on a Matlab figure axis copies... |
b82d814921fd81cde2d39384af88dd675d8335995be4f8ca22a4544a18664ea9 | MATLAB | 3,466 | 98 |
%==================== RetAngTuningDiagramFigure4.m ====================
% Plot Tuning diagrams for the mean response of neurons across 100ms Stim
% windows
%
%==========================================================================
close all
clear all
%================= SET PATHS AND LOAD DATA
if ismac
Pref... |
6054a7b210c1510be09d3a02b6444070ab60fd12170b7a1b7e00851bb35844fe | MATLAB | 3,467 | 79 | function PrepareMasksAndCohort(CurrentPath,CreateNewMask,Subregions)
% Creates explicit mask for image analysis.
% This function creates an explicit mask if it's non-existent at the
% location specified by CurrentPath or if CreateNewMask is set to 1 (e.g.
% because a new demographic information file was created at ... |
1ace7bbf26ad866c70bd12db4bb78df3896ab2b02b0d4156421732487afd8d39 | MATLAB | 3,470 | 92 | %% Fit Myelinated Fiber Density on Sural Nerve
load(fiber_distribution.builtin.data_path('jacobs1985.mat'));
% Prepare data
[xData, yData] = prepareCurveData( ...
age_vs_densityPerSqmm_myelinated_sural(2:end,1), ...
age_vs_densityPerSqmm_myelinated_sural(2:end,2));
% Set up fittype and options.
ft = ... |
b4c205efc145d313102eb66ecbfc842b7f640eafa1de13243ab85e4b8a14610a | MATLAB | 3,476 | 110 | function event = ft_read_event_tdt(tank,block,blockroot,eventname,eventvalue,Fs)
% EVENT = ft_read_event_tdt
% EVENT = ft_read_event_tdt(TANK)
% EVENT = ft_read_event_tdt(TANK,BLOCK)
% EVENT = ft_read_event_tdt(TANK,BLOCK,BLOCKROOT)
% EVENT = ft_read_event_tdt(TANK,BLOCK,BLOCKROOT,EVENTNAME)
% EVENT = ft_read_event_tdt... |
5a45a195dc0e59ca67e10f4d954613c386448a7530a0f240453dfbbf32cb5517 | MATLAB | 3,480 | 119 | function [data,time, t] = stimulate_TCS2(TCS2, volt_mat, ...
use_foreground, add_beep)
%
% In:
% TCS2 structure with params and initialized daq using
% initialize_TCS2.
% volt_mat \in (n_time_step, 8)
% use_foreground binary variable indicating to acquire data in
... |
cf49a85397fedaeba87212d898cf937b27f121d4f3a1b91978ff5a34c35b0b5b | MATLAB | 3,484 | 112 | %% Script to compare rinse and tastant trial beta values
% Rinse betas indices all_beatas 31:2:59
util.clearAll;
outdir = fullfile(util.get_paths().figs,'controls', 'rinse');
util.mkdir(outdir)
load(fullfile(util.get_paths().data_versioned, 'betas', 'full_beta_tbl.mat'))
% Find taste groups
[G, TID] = findgroups(fina... |
9b476368a0c0e3f42632d32bf60c2d9275e792826442d05aa6a26369f1351e5a | MATLAB | 3,495 | 94 | function [corrValues] = runCorrelations(corrBOLD_cat, paradigmNum, counter, dataDir)
% This function calculates the pairwise correlation between
% regions-of-interest (ROIs) as well as the partial correlations
%
% Compiler(s): Renee Hartig (renee.hartig@tuebingen.mpg.de) & Ali Karimi
% (ali.karimi@brain.mpg.de)
%
% Inp... |
cb9c43ee189c088b343284afde40c5db2fd93d94660c7f31402f7e2eb5463d8d | MATLAB | 3,499 | 102 | util.clearAll
beta = util.load.beta_table();
outdir = fullfile(util.get_paths().figs,'controls', 'correlation_Viz');
%% Get the Table entries for Left PrCo, left and right PAGs to demonstrate
% high and low correlations of beta series (0.92 vs 0.24)
PRCO_L = beta(beta.region_name == 'PrCo' & beta.hemisphere == 'L',:);... |
9248b9f159812495892f4436f766a47a8ff668bf5418e447db926dcd3d02a0de | MATLAB | 3,502 | 53 | function gamma_p = qtipm_get_gammap(c,l,D0)
%
% returns the 9x9 form of the matrix Gamma plus from the C 3x3x3x3 tensor
% C is expected to have already the correct units
%
gij = eye(3);
gij_1x6 = convert_3x3_to_1x6(gij);
scale = 0.25 * (D0^2);
d02gijgkl = scale * convert_1x21_to_3x3x3x3(convert_1x6_to_1x21(gij_1x6));
... |
e6461936c17b5f90ffba3577517384e694ced8839e8610bafc67f71a6312bb34 | MATLAB | 3,506 | 83 | %
% Define the tracts, sub-tracts their end-point ROIs using (one or more Destrieux labels)
% [tracts] = ccep_categorizeAnatomicalRegions()
%
% Returns:
% tracts =
%
%
% Note: Tracts are based on the Yeh HCP YA842 tractography atlas, while their end-point areas were matched based on the Destrieux... |
dbb301468f30284f4123b49f98b9f196995e79cb446ade47568ec4c0ec010f41 | MATLAB | 3,508 | 119 |
%% Script to calculate the phase-synchronization measures corrected with the surrogates
%This script calculates phase synchronization measures to study brain
%dynamics. The goal here is to describe the synchornization dynamics based
%on phase statistics. The present script computes four basic measures;
%integration, s... |
f07d657e06a5700350f7fe678f135a76e568049be194c4a8bafb0df848479884 | MATLAB | 3,509 | 113 | % Displays a dialog to give help information on an object.
%
% Examples:
% helpdialog char
% gives information of character arrays
% helpdialog plot
% gives help on the plot command
% helpdialog(obj)
% gives help on the MatLab object obj
%
% See also: helptext, msgbox
% Copyright 2008-2010 Levente... |
b42ba0a1aaad53a27deda4f4af37b70dad12db37a301aa6001ecd5554a25af11 | MATLAB | 3,511 | 123 | function [ERP, erpcom] = pop_saveERPhistory(ERP, filename, varargin)
erpcom = '';
if nargin < 1
help pop_saveERPhistory
return
end
if nargin==1
if ~isfield(ERP, 'history')
msgboxText = 'ERP.history was not found!';
title = 'ERPLAB: pop_saveERPhistory() error';
... |
970558ba8c54a01b1b4d5c5737948f338de25e5f2d2f9a36866bd420a5cf8750 | MATLAB | 3,515 | 119 | function coords = bilinearIntersection(cell1, cell2, v)
% BILINERINTERSECTION Finds the coordinates of the intersections of the
% V-level contour lines of unit squares CELLA and CELLB, calculated using
% bilinear interpolation.
%
% Inputs:
% CELLA must be a matrix of size [2 2] giving the values at the 4 vertices
% ... |
a1d46db45d366046576b9a6f1e2c42ca8ef5fbd9e516c3153534079e5587972f | MATLAB | 3,517 | 73 | function [FSC,FSCbs,ciLld,ciHld,ciLsc,ciHsc]=BSci(TmtxS,SCM,fnA,twin)
% Calculates bootstrapped confidence intervals on loading and activation of factor scores
%
% Core part of Factor analysis Assembly detection workflow
% NB Run FAassem_.m on unit firing rate data via runFAassem_.m first.
%
% Original 2014 Daniel Durs... |
929874d00d4f222fc9dd1b83e2b6144ba60784ce3a1a4ae4406d28ae2c0f7a8d | MATLAB | 3,521 | 100 | % DEPRECATED...
%
%
%
% EEG = lindetrend( EEG, interv);
%
% lindetrend():Removes the best straight-line fit from epoched EEG data.
% Matlab: detrend() computes the least-squares fit of a straight
% line to the data (whole epoch or interval) and subtracts the resulting function
% from the data (whole epoch).
%... |
6c94c5d3ad8941266ffbb79b2aa2f6a82745c37864ca4a94b65bf1619512a64f | MATLAB | 3,525 | 71 | %% Processes a single OH/OHA/TOH/TOHA trial
% This script converts a single trial into an event/state-based format,
% records known decisions, sets aside relevant metadata, and saves all of
% these for later analysis.
% Copyright (C) 2022 Richard Hugh Moulton
%
% This program is free software: you can redistribu... |
be1486b026df208bc3548da07dec4ec0a773702b8cee876a7a9bdf9d9cf2cd09 | MATLAB | 3,525 | 124 | load(['../data/behaviorData.mat']);
tmp = zeros(1,500);
hori_p = [tmp repmat(16.003,1,700)];
hori_n = [tmp repmat(8, 1, 700)];
vert_p = [tmp repmat(0,1,700)];
vert_n = [tmp repmat(-13.86,1,700)];
for n = 1:14
n
tDur = [1:1200];
tmp1 = cat(3, hori_p-Sub(n).dir(1).valid.hVel100, vert_p-Sub(n).dir(1).v... |
26564a2a9a5ce9cf00b0e860870cfcc4200af506058888e361e49bc5468af0e1 | MATLAB | 3,526 | 127 | function gr = lme_mass_RgGradient(X,Zcols,W,invH,L,phi,re,ni,invG,GDa,GDb)
% gr = lme_mass_RgGradient(X,Zcols,W,invH,L,phi,re,ni,invG,GDa,GDb)
%
% Gradient vector of the restricted log-likelihood for a whole region.
%
% Input
% X: Ordered design Matrix (according to time for each subject).
% Zcols: Vector with the ind... |
a3d7f69ad462387fd53fd1632a5762a34c4e3e938df4864e645f16809152a0f0 | MATLAB | 3,529 | 126 | classdef polyregions
properties
G %node graph
x %x coordinates
y %y coordinates
end
methods
function obj = polyregions(G,x,y)
%Constructor
s=G.Edges{:,1}(:,1);
t=G.Edges{:,1}(:,2);
w=sqrt((x(s)-x(t... |
c1aa04759d67913e42ac6daa6853b9d679022890f1c0a1b2d81f57808302d98d | MATLAB | 3,531 | 140 |
%function FM_sweep_testing()
% close all;
clear all
clc
%---FLAGS---%
sub = 4;
% Setup sound parameters
AMrate = 4;
AMdepth = 1;
StimDur = 1000;
%~~~~~~~~~~~~~~~~
AMphase = 0;
%~~~~~~~~~~~~~~~~
dBSPL = 50;
%~~~~~~~~~~~~~~~~
AMdelay = 500;
% Def3ne RCX file
% handles.RPfile = 'C:\gits\epsych\UserFiles\SanesLab\RPVdsCi... |
e9fb6adc58139027152e5987a1add41f052a0712d6a46044259e69db54a4aba1 | MATLAB | 3,531 | 106 | function val = artifactscantool_getopt(opt, key, default, emptymeaningful)
% FT_GETOPT gets the value of a specified option from a configuration structure
% or from a cell-array with key-value pairs.
%
% Use as
% val = ft_getopt(s, key, default, emptymeaningful)
% where the input values are
% s = str... |
755e56b8c0d0ad4cc1c88b427783b330cea2b20d1f2d8649c91796d5ad87c977 | MATLAB | 3,532 | 113 | % pop_create_custom_template() - Create a custom electrode montage template
%
% Usage:
% >> [STUDY, ALLEEG, com] = pop_visualareatemplate(varargin)
%
% Inputs:
% STUDY - STUDY set structure containing (loaded) EEG dataset structures
% ALLEEG - ALLEEG vector of EEG structures, else a single EEG datase... |
e0f39d3489b7bed7b8a5e3b8eb5014018c439d6826a479dbb8d538c3445cd7c9 | MATLAB | 3,533 | 142 | classdef o_ERPDAT < handle
properties
ALLERP
ERP
CURRENTERP
Count_ERP
ERP_chan
ERP_bin
Count_currentERP
Process_messg
erp_between_panels
Reset_erp_paras_panel
end
events
erpschange
drawui_CB
cer... |
9a52ba9db6dad225790891a462585ac42889e9369f510b94add661d0c7ac0725 | MATLAB | 3,535 | 98 | %% DEMO_001 basic useage
% The Psignifit 101
%% save data in right format
% First we need the data in the format (x | nCorrect | total)
% As an example we use the following dataset from a 2AFC experiment with 90
% trials at each stimulus level. This dataset comes from a simple signal
% detection experiment.
data = ... |
46233613edc62d09a75b2c4b9f61506be4f516c2c3732b7a24a5fb85624b26ea | MATLAB | 3,536 | 86 | %% This function calculates a subject's accuracy on a per-bin basis
% Subject accurady is divided between the easy/at-limit phases and the
% overwhelmed phase. Targets and distractors are considered separately.
% Copyright (C) 2022 Richard Hugh Moulton
%
% This program is free software: you can redistribute it and... |
ec486b9ebe08014e0d894e69aced66b14f5d58b658de83b74f278bb99429deea | MATLAB | 3,537 | 121 | % PURPOSE : encodes and retrieves ERPLAB's working memory
%
% FORMAT :
%
% output = erpworkingmemory(field, input2store)
%
% INPUTS :
%
% field - function name. e.g. 'pop_appenderp'
% input2store - values to store (cell array)
%
%
% OUTPUTS :
%
% output - stored values (cell array)
%
%
% EXAMP... |
dff6899efe539b677464f471898e1aeb415fb6db510b0190dc9d7a1cb5bad15b | MATLAB | 3,538 | 98 | function [ax1,ax2] = plot_stability( spikes, show)
% UltraMegaSort2000 by Hill DN, Mehta SB, & Kleinfeld D - 07/12/2010
%
% plot_stability - Plot amplitude and firing rate of a set of spikes over time
%
% Usage:
% [ax1,ax2] = plot_stability( spikes, clus)
%
% Description:
% Creates two axes in the same posit... |
7135ec6ebf3a80277a9fa9e5592f6ed97516af3710fea09f15ccd478e1c7d4b0 | MATLAB | 3,541 | 72 | function [samples_file_format, totalParams] = getSampleFileFormat(obj, TotalSamples, dataType_samples, paramStruct, scaled_WB, scaled_VT, saveUnscaled)
samples_file_format = cell(0, 3);
ctr = 1;
totalParams = 0;
samples_file_format{ctr, 1} = dataType_samples;
samples_file_format{ctr, 2} = [numel(paramStruct.W) TotalS... |
8061c4a1797102d097424d005520235dc39092783a7aff05ea754b0f4677e71f | MATLAB | 3,542 | 83 | clear
Target = 'LONG';
if ispc
pat = 'C:\Analysis\AssemblyAnalysis\raw';
else
pat = '/Volumes/HDD2/DNMTP/raw';
end
cd(pat)
fileList=dir(sprintf('allTimestamps%s*%s*Events.mat',filesep,Target));
% reject_list={'IreneuszLONG1_Events.mat',...
% 'NorbertMEDIUM1_Events.mat',...
% ... |
dd4dbdc7e64b6df85b5c6797c277c3d6d71f1404d008abe67b25b43153f4bb8e | MATLAB | 3,542 | 98 | function [rowcoords, colcoords, patType, jacobians] = classifyCrit(vx, vy, edgeDistance)
% CLASSIFYCRIT finds and classifies the critical points in the vector field
% defined by VX and VY. Outputs 2 1xN vectors (where N is the number of
% critical points detected) expressing the row and column coordinates of
% e... |
57d79d38fef7ebdf8861ac918570cdf2c79ac4e325036647b9d49649291be2f1 | MATLAB | 3,546 | 121 | function NextTrialID = TrialFcn_AMAversive_MasterHelper(TRIALS)
% NextTrialID = TrialFcn_PumpControl(TRIALS)
%
% This is the default function for selecting the next trial and can be
% overridden by specifying a custom function name in ep_ExperimentDesign.
% The code in this function serves as a good template for custo... |
b6331afa5988ef2b3c0a13351a10eb21aba5825b3acef14165909268a41509d9 | MATLAB | 3,547 | 133 | clear all
clc
%% Selection of the peak folder
start_folder = uigetdir(pwd, 'Select the PeakTrains_mat folder');
if isempty(strfind(start_folder, 'PeakTrains_mat'))
f = errordlg('Folder not corrected', 'Folder Error');
return
end
disp(start_folder);
cd(start_folder);
phase_dir = dir;
if length(phase_dir) == 2
... |
d98cee8f5e0e192bc275188bda2f6d21f76b3c5e7ca51afc62ddd2f7028aea7a | MATLAB | 3,564 | 106 | function iCross = plot_cross_section(model, ax, fascClickCallback)
%LOAD_CROSS_SECTION Summary of this function goes here
% Detailed explanation goes here
if nargin < 3
fascClickCallback = @(~, ~) [];
end
% Choose z closest to the active site
z = model.activeSites(model.iAS).coord(3);
zs = cellfun(@(x) x(1,3), ... |
fe685dc1cb4a4e1b0aa7a732e5889e4aae4fa5cd4b976144722fece6ede7c33d | MATLAB | 3,566 | 112 | function [] = scatter_sequence(all_trials, s,varargin)
% Display the input sequence on the current axes.
% Default plot parameters
mSize = 16 ; %
colors = [0,0,179; 255,67,46]./255 ;
small_version = 1 ; % no labels for the 2 I
cond_name = '' ; % ticklabels in smal... |
7fabfdd28de04f723259c14af171f0b94ac821d4c854a9e8dc76c26a948f7422 | MATLAB | 3,571 | 143 | function model = dtipm_data2fit_SDPdSL(signal,bten,varargin)
% function model = dtipm_data2fit_SDPdSL()
%
% out_flag says which format to use for m :
% out_flag = 1 -> [28*nvox,1]
% out_flag = 0 -> [28, nvox]
nmeas = size(bten,1);
% r... |
bc020a035f820ed82c6f1b2616a5c5ca2f65cde858c1e3559100481dbe143a73 | MATLAB | 3,571 | 107 | function varargout = updateRUNTIME_SanesLab(varargin)
%Custom function for SanesLab epsych
%
%This function updates the RUNTIME structure and parameters for next trial
%delivery.
%
%Inputs:
%varargin{1}: RUNTIME structure. If not passed as input, RUNTIME is called
% as a global variable.
%varargin{2}: han... |
f5ccddf6f0d4aa8cb2550f3040d0944d43acf104163a0cc9cdf5cde5b2e08075 | MATLAB | 3,572 | 93 | function [electrode, activeSites] = import_electrode_geom(direlec, felec, fFEM, cross_pl)
% IMPORT_ELECTRODE_GEOM Imports the electrodes contour and active sites.
% The code import the .STL files of the electrodes and convert the geometry
% file in a 3D representation of the electrode corners and center of active... |
2fbf95354cd5a9463224510d466f559ec1b6077af0185126de4ec131e5691697 | MATLAB | 3,573 | 156 | % Philipp Berens
% CircStat: A Matlab Toolbox for Circular Statistics
% Submitted to Journal of Statistical Software
%
% Example 2
% An Application to Neuroscience
%
%
% In this example, we assess the orientation tuning properties of three
% neurons recorded from the primary visual cortex of awake macaques. th... |
719ea279fffdc6f465c8104402305fb2537f8800bc28cd8ccd5d5f49768211b3 | MATLAB | 3,577 | 131 |
function Stim = pp_make_stim_struct( epData, block )
%
% pp_make_stim_struct( epData, block )
% Sub-routine called by pp_prepare_format.
%
% Creates matlab struct with number of elements equal to number of
% trials, and fields with stimulus information for each trial.
%
% This function should be ... |
ab0b318f8fb5728ca84c671934f37024f80922c4cf8507457eb02706bd6e00a9 | MATLAB | 3,577 | 92 | %% Additive Workload Serial System
% A parallel-serial processing system where different tasks increase the
% amount of work to be done by certain modules by an additive amount
%
% 3 December, 2021
function [finalRate,input_record,output_record] = AdditiveWorkloadSerialSystem(systemCapacities,taskModifiers,visualiz... |
c6553ca901dafca971e2ba3191459c6d1ed1357ad8f7ec68a9dc7160ed8f1d98 | MATLAB | 3,579 | 92 | %% Multiplicative Workload Serial System
% A parallel-serial processing system where different tasks increase the
% difficulty of certain modules' processes in an multiplicative manner.
%
% 3 December, 2021
function [finalRate,input_record,output_record] = MultiplicativeWorkloadSerialSystem(systemCapacities,taskMod... |
173b8fe5c9d91c75a04816e3ebecf9a75817edfa24422d8bf2bf722239a26586 | MATLAB | 3,580 | 165 | % PURPOSE: pop_suffixeeg.m
% add suffix to ALLEEG names
%
% FORMAT:
% [ALLEEG, erpcom] = pop_suffixeeg( ALLEEG, 'suffixstr',suffixstr,...
% 'Saveas', 'off', 'History', 'gui');
% Inputs:
%
%ALLEEG -ALLEEG structure
%suffixstr -strings for eegsets
% *** This function is part of AL... |
75b8fa4c86068ae32835aab517d15de7f9356dab3b99367a06217f72f3bcae12 | MATLAB | 3,585 | 104 | % DEPRECATED...SORRY.
%
%
%
% PURPOSE : The purpose of this function is to allow multiple dataset loading,
% while user is working on the EEGLAB GUI. Do not use this function
% in scripting. Use pop_loadset() with a for loop instead.
%
% FORMAT :
%
% >> [ALLEEG EEG CURRENTSET] = pop_loadm... |
784f5aa1f9d6275f799305d7ac475b62bd672d14fbf50929d12e0a01e4e92a62 | MATLAB | 3,589 | 130 | function varargout = DB_NewSubjPrompt(varargin)
% h = DB_NewSubjPrompt
% h = DB_NewSubjPrompt(database)
%
% Create New Database Subject. If database name is not supplied as input
% then a list dialog will prompt the user to select a database.
%
% DJS (c) 2010
%
% Last Modified by GUIDE v2.5 10-May-2013 13:10:04
% ... |
e1cb85f6126eefaecdee1a95605b12446b100d092d8a8894a51b639b5f16ce58 | MATLAB | 3,592 | 128 | addpath('/useful functions/');
velocity= importdata('./kymo_ex_data/resultats.mat');
dxpix = 0.955; % Pixel size in um
dttime = 5; % Time step in minutes
vscale = (dxpix/dttime);
xlag = velocity.XEul;
ylag = velocity.YEul;
ulag = vscale*velocity.UEul;
vlag = vscale*veloc... |
4d04afbdce39d43ab7efba0ef9510e227069b163c682605cfda5de926dcc8173 | MATLAB | 3,596 | 113 | function X = expsmooth( X, fs, tau )
% EXPSMOOTH Exponential smoothing.
%
% Y=EXPSMOOTH(X,FS,TAU) for a given input sequence X sampled
% at FS Hertz and for time constant TAU given in milliseconds
% returns exponentially smoothed output sequence Y.
%
% Inputs
% X input signal as a column vector, or... |
b57a187c35d55dede05908f5a172acd5d622ec323ebd7e3cbed088e2944a0666 | MATLAB | 3,596 | 113 | function [ims,channels] = tppreview_timethreshaverage(dirnames, tpparams, channellist, parameters, shortname, dirname)
% TPPREVIEW_TIMETHRESHAVERAGE - Make a preview image based on thresholded temporal differences
%
% [IMS,CHANNELS] = TPPREVIEW_TIMETHRESHAVERAGE(DIRNAME,TPPARAMS,CHANNELLIST,PARAMETERS)
%
% Inputs:
% ... |
6a5bf0bf94a81773e2fdd73a3a6ca6706781cc3463b6f3129314cfae63a96185 | MATLAB | 3,600 | 156 | function F = gan_img_detection_fea(IMG)
%GAN_IMG_DETECTION_FEA Extract features for detecting GAN generated images.
%
% Input:
% - IMG: An image array or a path to the image file.
%
% Output:
% - F: The 588-D feature for GAN generated image detection.
%
% The algorithm is proposed in the following paper:
% @article{DB... |
32e9609ac9f207a77a8035ab941de454670126f1cb6765027fc8046337ab0ea8 | MATLAB | 3,601 | 104 | % Intraparietal stimulation disrupts negative distractor effects in human multi-alternative decision-making
% Kohl, C., Wong, M.X.M., Wong, J.J., Rushworth, M.F.S. & Chau, B.K.H.
% eLife 2022
% Script to generate Figures 3d & 3e
clear all; close all; clc;
% Load betas generated from GLM3 (Figure 3abc)
load(... |
887f4a14bcd5096e0a6103552094242fde3f24838e7c24354aa8ed8c7783a0b2 | MATLAB | 3,601 | 90 | function [swEsts, nswEsts, swLabels, nswLabels, bias_means, bias_stdevs] = simulateSwitchNoSwitch(nameValueArgs)
arguments
nameValueArgs.settings struct = readSettings();
nameValueArgs.sampleNums (:, 1) double = -1; % -1 means all
nameValueArgs.runParallel logical = true;
nameValueArgs.plot logi... |
5aa7b25ce8a3ceba8d30c300ba1fe28694afe0f2b27a23b22591c012ceba4d3a | MATLAB | 3,602 | 91 | function [spikes, new_clust] = split_cluster(spikes, subclusters)
% UltraMegaSort2000 by Hill DN, Mehta SB, & Kleinfeld D - 07/12/2010
%
% split_cluster - split a cluster into two parts
%
% Usage:
% [spikes, new_clust] = split_cluster(spikes, target)
%
% Description:
% Breaks off the specified sub-tree from the... |
0f8a9dc495cc6f4e4bd391ecbebcc85bc41e8e30d2afc1084f6602100fab3f0b | MATLAB | 3,611 | 99 |
%==================== RetAngSDFFigure4.m ====================
% Plot the mean SDF for all neurons to examine time based responses
%
%==========================================================================
close all
clear all
%================= SET PATHS AND LOAD DATA
if ismac
Prefix = '/Volumes/nifvault'; ... |
6063ca3ee53db84b64fcd3d9e6b9484e7f7d2011dde75dcf4df4411b35bd4e43 | MATLAB | 3,612 | 83 | function [FSC,FSCbs,ciLld,ciHld,ciLsc,ciHsc]=BSciSleep(TmtxS,SCM,fnA,twin)
% Calculates bootstrapped confidence intervals on loading and activation of factor scores
%
% Deals with long time-series typical of sleep recordings rather than short single-trial behavioural data.
%
% Core part of Factor analysis Assembl... |
1ec735e4f86af064e56b9da2beb631a297f2f740a53ae2d23a290573ba1eef45 | MATLAB | 3,613 | 104 | function [qe,Ee,Se,Sev] = qeh8e(En,Ge,Ue,Sn,Set,Xe)
%***************************************************
% Keh8E:
% Creates the element elastic forcee vector for
% hexahedra 8-node element.
% Syntax:
% Ke = qeh8e(Xe,Ge)
% Input:
% Xe : coordinates Xe = [x1 y1; x2 y2; x3 y3; x4 y4]
% Ge : element ... |
2d62798e86fb7e217e158be3070c84a534e12f5ddb5434550f71e4dcf6a690ce | MATLAB | 3,614 | 52 | function gamma_m = qtipm_get_gammam(c,l,D0)
%
% returns the 9x9 form of the matrix Gamma minus from the C 3x3x3x3 tensor
% C is expected to have already the correct units
%
gij = eye(3);
gij_1x6 = convert_3x3_to_1x6(gij);
scale = 0.25 * (D0^2);
d02gijgkl = scale * convert_1x21_to_3x3x3x3(convert_1x6_to_1x21(gij_1x6));... |
144757e6bc11a15a83cd43a673494e425900ea594ada1f2d026405d163800f33 | MATLAB | 3,622 | 100 | % Plot the L/R preference of each assembly.
%
% Aleksander PF Domanski PhD UoB 2015
% aleks.domanski@bristol.ac.uk
%
% Need data from runFAassem first.
clear
cd('C:\Analysis\AssemblyAnalysis\raw\KDE_bins\LONG')
fn='JaroslawLONG2_iFR50_FSC.mat';
% fn='KrzesimirLONG2_iFR50_FSC.mat';
twin=10; % Time w... |
62c9480e3a68acea2552a7266b7a97b8670bfa98a30adc076ee37185e25d3c5e | MATLAB | 3,623 | 113 | function masked_files = MySPM_BatchMasking(fmri_fns,mask_fn)
% MySPM_BatchMasking
% MySPM_BatchMasking(fmri_fns,mask_fn)
% d = MySPM_BatchMasking(...)
%
% Use this script to apply a mask to one or more 3D or 4D NIfTI files.
%
% Input: fmri_fns ... cellstr array of 3D or 4D NIfTI files (optional)
% m... |
4170086eb75e21d3ea8c9f3a46d55a36d26f685d9531b3df7c032fa170a40a04 | MATLAB | 3,630 | 114 | function [ transitionMatrix columnStates ] = getTransitionMatrix(markovChain,Norder)
% Constructs the transition matrix of a markov chain, given the markovChain and the order, i.e., an integer greater or equal to 1.
%
% Inputs:
% markovChain : the markov chain, in integers.
% Norder : the order to be analyz... |
5ef9a9af5ae72fde997baee029aba3c920728f8474aead52a18c9f6708ea3865 | MATLAB | 3,632 | 117 | function AX = ReferencePhys_SanesLab(handles,AX)
%ReferencePhys_SanesLab(handles)
%
%Custom function for SanesLab epsych
%
%This function performs the calculations necessary for the common signal
%averaging for multi-channel recordings.
%
%Inputs:
% handles: GUI handles structure
% AX: handles to active X controls... |
488d1f49f31362e809015778ad8d333734bc7fe58269503c5c3b8e96c0c721e6 | MATLAB | 3,635 | 122 | clear
subjfolder = dir('F:\fMRI_QC\fmri-open-qc-task_bias_corrected\sub*');
%figure('WindowState','maximized');
figure('position',[10 50 1500 500]);
for subji = 1:length(subjfolder)
fprintf('Processing subject %d ...',subji)
% load the raw functional images and calculate the global mean and pairwise vari... |
e87ebbc53549b66274ee8849481b1c8575686284d5f9c1b7fc14f870aaa49b32 | MATLAB | 3,638 | 95 | function b = suite2ptifs2prairieview(suite2p_exper_dir, new_exper_dir, directory_mapping, channel_mapping, doit)
% SUITE2PTIFS2PRAIRIEVIEW - convert a set of suite2p registrations back to PrairieView
%
% B = SUITE2PTIFS2PRAIRIEVIEW(SUITE2P_EXPER_DIR, NEW_EXPER_DIR, ...
% DIRECTORY_MAPPING, CHANNELMAPPING, DO_... |
2ca25d68d71714a821bc3cec6ea606f9933cd88f17381009045ab5a88e0b426e | MATLAB | 3,646 | 120 | % PURPOSE : encodes and retrieves ERPLAB's working memory
%
% FORMAT :
%
% output = estudioworkingmemory(field, input2store)
%
% INPUTS :
%
% field - function name. e.g. 'pop_appenderp'
% input2store - values to store (cell array)
%
%
% OUTPUTS :
%
% output - stored values (cell array)
%
%
% E... |
353c622f1f7bcb2c396d9a44fff4881da2cb8ecc3f96e78e772d097eb9601a4b | MATLAB | 3,646 | 74 | %% GMLM.computeMAPevidenceOptimization
% optimizes the log-evidence (plus log hyperprior) of the GMLM using quasi-newton optimization & Laplace approximation for the evidence
%
% inputs:
% params_init (OPTIONAL) :a param struct of the initial value of the optimization. If not given or empty, a random initiali... |
29729488416b7785c6366160526a3a5b011759c36e4ff42eafdf177917270263 | MATLAB | 3,651 | 79 | function [signal_data, data_legend, t] = createDataMatrix(raw_data, data_start, ...
framerate, t_window, t_parameters)
% createDataMatrix cleans up raw imported data and returns key variables
% Implements any raw_data parameters from "Ca_Pipeline_Main.m"
% and outputs a new matrix, legend, and time vector for t... |
97bd6712edf8d8015515505f5f0fea42f85a721b9fabb8a228d15dbeca997c39 | MATLAB | 3,656 | 138 | function model = qtip_data2fit_SDPdc(signal,bten,varargin)
% function model = qtip_data2fit_SDPdc()
%
% out_flag says which format to use for m :
% out_flag = 1 -> [28*nvox,1]
% out_flag = 0 -> [28, nvox]
nmeas = size(bten,1);
... |
531ca2dfec07ef6d040b61833df5b0a1f9650d6b391fc6dddcb9ae54b252203b | MATLAB | 3,664 | 102 | function popupmore(fh,varargin)
% SUBPLOT POPUP FUNCTION WITH ADDITIONAL ARGUMENTS
% makes use of the function POPUP and PVPMOD
%
% EXAMPLES
% popupmore(fh) => popup(gca); standard function
% popupmore(fh,'lg',???) ... |
2bc58b8fefdcdb4c6eb9804f9c2a0c36802ae5ad967b4d05245e34804406e42d | MATLAB | 3,672 | 134 |
%% Script to generate Figure 4
clear all
close all
runs = 10;
epochs = 1000;
% folder1 = 'Experiment1';
% folder2 = ['RNN', 'LSTM', 'GRU'];
% folder3RNN = ['16','64'];
% folder3GRU = ['8','32'];
runsstrings = {'Run1','Run2','Run3','Run4','Run5',...
'Run6', 'Run7','Run8','Run9','Run10'};
% RNN
rmseRNN16T = zeros... |
c6a9e603a701db0359e894f84482a2337f99eda6d7be0b901057aac436199d9b | MATLAB | 3,674 | 81 | function [FSC,FSCbs,ciLld,ciHld,ciLsc,ciHsc]=BSciTaskOnly(TmtxS,SCM,fnA,twin)
% Calculates bootstrapped confidence intervals on loading and activation of factor scores
%
% Deals with long time-series typical of sleep recordings rather than short single-trial behavioural data.
%
% Core part of Factor analysis Assem... |
969673b0109771d341240d4e71f2a52b1c4f6d819d2db5d2380ee74f2b91a02c | MATLAB | 3,683 | 137 | %-------------------------------------------------------------------------------
% resample_eeg_files: resample all files
%
% Syntax: resample_eeg_files(eeg_dir, out_dir, fs_new, lpf_cutoff)
%
% Inputs:
% eeg_dir - directory of EEG files (in CSV format); required
% out_dir - empty directory for the dow... |
c6c1a1ea7960c0a00c07d618a810bf1cfeceaad9420715bf55b75f96200af783 | MATLAB | 3,684 | 106 | function eda_stat_boxplot(eda, fs, edr, conds)
% EDA_STAT_BOXPLOT Plot EDA results
% EDA_STAT_BOXPLOT(eda, fs, edr, conds)
%
% Required input arguments:
% eda - 1-by-n vector of EDA samples
% fs - sampling rate (Hz)
% edr - structure array of electrodermal response (EDR) (see eda_edr.m)
% cond... |
7abdd771476f8b3170cd800718dcd8a1eb34a91bffaff3bb0a971a658dcee8f6 | MATLAB | 3,686 | 98 | % PURPOSE: subroutine for pop_setcodebit.m
% sets the bit(s) at position(s) "bitindex" in each EEG.event(i).type value to 0 (off).
% "bitindex" must contain number(s) between 1 and 16.
%
% EEG = setcodebit(EEG, bitindex, newvalue) sets the bit(s) at position(s) "bitindex" to the value "newvalue", ... |
87c7a5ffddc84c7e5b1e7be609cc5896367a61e4c3a639861b787ce04dc520d5 | MATLAB | 3,688 | 164 | % PURPOSE: pop_suffixmvpc.m
% add suffix to ALLMVPC names
%
% FORMAT:
% [ALLMVPC, mvpcom] = pop_suffixmvpc( ALLMVPC, 'suffixstr',suffixstr,...
% 'Saveas', 'off', 'History', 'gui');
% Inputs:
%
%ALLMVPC -ALLMVPC structure
%suffixstr -strings for bestsets
% *** This function is pa... |
ade059dd5740bfb5d7103d67d33d20e52fbfd85cc6463501df88760f5d239816 | MATLAB | 3,688 | 119 | function [Gw,Gs,Gss]=geombinsurr_partial(W,D,frac,nbins,bintype)
% [Gw,Gs,Gss]=geombinsurr_partial(W,D,frac,nbins,[bintype])
%
% Surrogate random graphs that approximately preserve the relationship
% between weight and distance by first binning the edges by distance and
% then shuffling within the bins. Randomizes... |
d32d73d6190f751b8bbf065ca9229d343bbd3f3a1321ca0d51760c11d077cb1c | MATLAB | 3,696 | 101 | function [Ke,qe] = keh8e(Ee,Ge,Se,Xe,Set)
%***************************************************
% Keh8E:
% Creates the element stiffness matrix of viscoelastic
% hexahedra 8-node element.
% Allows elastic and viscoelastic behaviour with Kelvin-Voigt (parallel
% elastic-dahspot) and Maxwell (in series).
% ... |
cad5f250ec76b2e47cda2f601112e4956e7bbc24c4d2c38d7164c474e416b090 | MATLAB | 3,698 | 97 | function lrstats = lme_LR(lrmlfull,lrmlred,q)
% lrstats = lme_LR(lrmlfull,lrmlred,q)
%
% Likelihood ratio test for the random effects. It can be used to test if a
% model with q+1 random effects is significantly better than a model with q
% random effects.
%
% Input
% lrmlfull: Maximum value for the restricted log-like... |
07938d7421a4af4ac736f5ea988bb38d92c8e530de2891aebfa487202b0d20aa | MATLAB | 3,700 | 124 | function NextTrialID = TrialFcn_AMAversive_MasterHelper_ROSEN(TRIALS)
% NextTrialID = TrialFcn_PumpControl(TRIALS)
%
% This is the default function for selecting the next trial and can be
% overridden by specifying a custom function name in ep_ExperimentDesign.
% The code in this function serves as a good template for... |
4d169aece7509e0963828d68fdec28525022c0ddadfc6db5534c02180e9612cc | MATLAB | 3,702 | 110 |
% finalDynamicsStream
% validationModel
% validationEmission
% returns likelihood (bootstrapped likelihood
if size(validationEmission, 2) ~= size(finalDynamicsStream,2)
disp(['Emission matrix must be STATES by CHANNELS (' num2str(size(validationModel,2)) ', ' num2str(size(finalDynamicsStream,2)) ')']);
retur... |
49689e84492c647635a5020c21526e71e604854668b469c7c340351f204a3cd5 | MATLAB | 3,704 | 140 |
function pp_prepare_format(BLOCKS,subject,session_label)
%
% pp_prepare_format( BLOCKS, subject, session_label )
% Creates data structures in the desired format for processing. Groups
% together sequentially-recorded blocks, indicated in input argument,
% and makes a structure with stimulus info by trial, ... |
7b51fee7e59abcf6b14457e670625c25b43bc6a62dd8f813b53ece41c58a7334 | MATLAB | 3,705 | 105 | function check_session_TCS2(NI_session, pulse_dur, temp_base,...
temp_I1, temp_I2, active_zones, fn_check, subj_name, record_RT)
% Check session: sequence of stimuli of 2 intensities, subject has to
% evaluate the intensity received and RT is recorded.
% Parameters %%%%%%%%%%%%%%%%%%%%
p = [0.5,0.... |
33f7034aad9cd490935d73b0e6b2a8e2273f141288feb6e34f92f8298f228b28 | MATLAB | 3,707 | 95 | %% Preamble, get file list
clear all; close all
set(0,'DefaultFigureWindowStyle','docked')
flags.plotIndividualChanges = false;
% pat{1} - % location of the processed assembly memberships
% pat{2} - % location of raw spike times
if ispc
% pat{1} = 'C:\Analysis\AssemblyAnalysis\Sleep\Decoding vs flanki... |
3bc1e13c60010c5f3466d29a278fda8d981c6950cbf17ba7bd63badd467bd1a5 | MATLAB | 3,708 | 158 | function varargout = PumpControl_Tunings(varargin)
% PUMPCONTROL_TUNINGS MATLAB code for PumpControl_Tunings.fig
% Edit the above text to modify the response to help PumpControl_Tunings
% Last Modified by GUIDE v2.5 23-Sep-2015 10:31:06
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct... |
a1094fcd07ea2c1d20e8d8cf5591f494a085e054765793479b7ac2b27c371630 | MATLAB | 3,708 | 163 | % PURPOSE: pop_suffixbest.m
% add suffix to ALLBEST names
%
% FORMAT:
% [ALLBEST, bestcom] = pop_suffixbest( ALLBEST, 'suffixstr',suffixstr,...
% 'Saveas', 'off', 'History', 'gui');
% Inputs:
%
%ALLBEST -ALLBEST structure
%suffixstr -strings for bestsets
% *** This function is p... |
4ce30a1d7cd48580e295ffa236ff893d16317757377d558183cf01c45df2c22c | MATLAB | 3,713 | 143 | function Problem = l1_linear_svm(x_train, y_train, x_test, y_test, lambda)
% This file defines l1-regularized SVM problem
%
% Inputs:
% x_train train data matrix of x of size dxn.
% y_train train data vector of y of size 1xn.
% x_test test data matrix of x of size dxn.
% y_test ... |
d6c423c60428d103bf1344b95aabbf8409a541571c657d5fe758803acc5e06ba | MATLAB | 3,713 | 153 |
function FMdepth_detection()
clear all; clc; close all;
handles.RPfile = 'C:\gits\epsych\UserFiles\SanesLab\RPVdsCircuits\KP\FM_sweep_test.rcx';
%Load in speaker calibration file
% [fn,pn,fidx] = uigetfile('C:\gits\epsych\UserFiles\SanesLab\SpeakerCalibrations\*.cal','Select speaker calibration file');
fidx=1;
pn = ... |
1efe051a355d568c16282da7e5349c8eb306728ff9a3439e7585869103fc6d75 | MATLAB | 3,715 | 137 | % fresh start
clearvars
close all
%% run config
config_file='config_mammals_1.m';
addpath(strcat(pwd,'/config'))
run(config_file);
%% setup vars
thr_vals = [ 0 0.05 0.1 0.15 ] ;
ff = [ PROJ_DIR '/reports/lab_meeting/animal_colors.mat' ] ;
load(ff)
odir = [ PROJ_DIR '/reports/figures/netdist/' ] ;
mkdir(odir)
fo... |
cb25cbd7eeb2496e8d7ec9212a2fc303e745faf48c8cfe7e893b5c2def707276 | MATLAB | 3,717 | 106 | function [Vs, FEM] = load_pot_per_AS(model, fibersCompart, fascIdsByAs, activeSites, iActiveSite)
% LOAD_POT Loads FEM computed stimulation potential for all the x,y points
% of the fibers in the population. Values on the z axis are linearly spaced
% until the maximum z point possible in order to perform interpolati... |
4c072d04cf6432f1993ac0616980ba6add49dd1d460cab47bee91d89ebf05fe0 | MATLAB | 3,720 | 113 | function [im] = tpcheckroidrift(dirname, channel, roirect, roiinds, roix,roiy,roiname, plotit)
% TPCHECKROIDRIFTNAME - Checks twophoton drift correction performance
%
% IM = TPROIDRIFT(DIRNAME,CHANNEL,ROIRECT,ROIINDS,ROIX,ROIY,RIONAME, PLOTIT)
%
% Checks drift correction performance. Takes a rectangle (ROIRECT) as... |
c2a02f119717a9fd511ebc6e65f5a4fc188bd3dc40b0c4244bc486c1a6b5a07e | MATLAB | 3,721 | 76 | function RunQUIQI(Subregions,Lambda,DataType,AnalType)
% Main function enabling the insertion of a motion degradation index into
% the analysis of MRI data.
%
% INPUTS:
% - Subregions: cell array with the list of tissue types to be analysed
% p1: grey matter
% ... |
4fbe836ff92edfdaaedb7f7ad6a5d68b07ce24562c5110319c84ba71b8146c4b | MATLAB | 3,722 | 88 | % Return java.lang.Class instance for MatLab type.
%
% Input arguments:
% mtype:
% the MatLab name of the type for which to return the java.lang.Class
% instance
% ndims:
% the number of dimensions of the MatLab data type
%
% See also: class
% Copyright 2009-2010 Levente Hunyadi
function jclass = ... |
3cfbf9b65b75659316766cd6125dfdf9fa24a1853c06ff0285f8e9f32684fb49 | MATLAB | 3,723 | 153 | function updateTimeline_WE(width)
%
% Function used to continuously shift the timeline slightly ahead of the
% current time every two seconds.
%
% width - time window in seconds in which show of events
%
global DA gf h
fig = h.timelineF;
ax = h.timelineA;
% X axis
xMax(2) = ceil(gf.sessionTime); % session tim... |
5e11cb9e4f071b40d4ad0ea6daa045ce6e4ed446f9de4ed5392f412747c0a970 | MATLAB | 3,726 | 95 | function effectSize = calculatePEV(tbl,value,repeated)
%%
%effectSize = calculatePEV(tbl,value)
%
% This function calculates the percent explained variance of a factor in a
% one-way or two-way ANOVA (omega2 and partialomega2 respectively).
%
%INPUTS
% * 'tbl' : ANOVA table (-> anovan)
% * 'value' ... |
0d94686681bdff03e3e205f0ad4635c766f83f4ee8e5e13328d6c11a4bc434fb | MATLAB | 3,728 | 117 | function createNozzleProblem(filename, channel_leftwidth, channel_rightwidth)
% This function creates a nozzle shape, a channel of a varying width at
% both ends. Emerging from the nozzle out into unobstructed tissue presents
% a situation of source/sink mismatch that can possibly trigger conduction
% block.
% Define... |
6be5b1ca35b48378152b3f2b721e447c4fcf73b5b205897b0f139bef01cb9a0b | MATLAB | 3,738 | 85 | function Noise = NoiseExtractFromImage(image,sigma,color,noZM, residual_dir, confidence)
% -------------------------------------------------------------------------
% Copyright (c) 2012 DDE Lab, Binghamton University, NY.
% All Rights Reserved.
% ---------------------------------------------------------------------... |
5be4a0e552e39ba89120b1c451e1436e0b17ffad20a00e82684151402ba58cb7 | MATLAB | 3,740 | 127 | function f = calccod(x,y,dim,wantgain,wantmeansub)
% function f = calccod(x,y,dim,wantgain,wantmeansub)
%
% <x>,<y> are matrices with the same dimensions
% <dim> (optional) is the dimension of interest.
% default to 2 if <x> is a (horizontal) vector and to 1 if not.
% special case is 0 which means to calculate glo... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.