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ad1db083def524214fb002612c44b6fc2d421f1fe6ac92551487664677af4209
MATLAB
1,545
61
classdef Annotation properties ProjectPath VideoName File FilePath AnnotationTable Behaviors MultiCam = false; PrimaryCamera = '' CameraNames end methods function self = Annotation(project, video) ...
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MATLAB
1,545
41
function tbread(table,cols,vecs,sql) % tbread Read from MySQL table [mym utilities] % Inputs table - table name, string % cols - list of input columns, (m*1) cell array of strings % vecs - list of output vectors, (m*1) cell array of strings % sql - SQL 'select' stateme...
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MATLAB
1,547
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function visualCart(h,x,Target,Head,Tol) persistent p p2 %Define the shape and colour of the dot based on elevation and target %heading if x(6) <= -15 dotColour = 'b'; dotMarker = 'o'; elseif x(6) <= 15 if (x(5) > (Head(Target) - Tol(Target))) && (x(5) < (Head(Target) + Tol(Target))) dotColour = 'g...
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MATLAB
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function [filteredData] = filterData(data, sigma, kernel, noFlip, paddingMode) % paddingMode = 0 -> Pad with repeated values % paddingMode = 1 -> Pad with 0s % paddingMode = 2 -> Pad circularly if ~exist('noFlip', 'var') || isempty(noFlip) noFlip = false; end if ~exist('paddingMode', 'var') || isempty(paddingMod...
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MATLAB
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function plotPredFace(predDat,weightsPixels,rootDir) if ~exist('rootDir','var') rootDir = []; end nMice = numel(predDat.ypred_test); W_all = predDat.W_all; % Weights for best predictions pc2plt = 1; figure; for k = 1:nMice subplot(ceil(sqrt(nMice)),ceil(sqrt(nMice)),k)...
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MATLAB
1,556
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% PURPOSE: erases ERPLAB Studio's memory (values are those last used. Default ones are reloaded) % % FORMAT % % erplabamnesia(warningop) % % INPUT: % % warningop - display warning message. 1 yes; 0 no % % % *** This function is part of ERPLAB Studio Toolbox *** % Author: Guanghui Zhang % Center for Mind and Bra...
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MATLAB
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function generate_patches(cropped_size, overlap, pixel_threshold, var_threshold, ... save_all, source_path_3d, save_path_3d, source_path_2d, save_path_2d, bitdepth) % GENERATE_PATCHES crops small 3-D stacks and corresponding 2-D light field % raw image for training. It discards the patches lack of information based...
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MATLAB
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function result = addTankToRegistry (tank, directory) % AddTankToRegistry Adds a given tank to the TTankEng through the registry % % result = addTankToRegistry (tank, directory) % Given the string tank name (i.e. '070515A') and the string directory % to the tank (i.e. 'C:\Tanks\') with a trailing backslash...
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MATLAB
1,559
66
function NHP_SaveDataFcn(RUNTIME) % ep_SaveDataFcn(RUNTIME) % % Default function fo saving NHP sound localization data. Also generates % and plots psychometric function fit (estPsychFnc). Results from fit are % saved as Data.res (Data.res.Fit = [threshold,width,lambda,gamma,eta]) % % Daniel.Stolzberg@gmail.com 8/20...
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MATLAB
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59
function [ w_min, f_min, f_max ] = draw_3D_surface(cost, n, x_min, x_max, y_min, y_max) % Draw 3D surface. % % Inputs: % cost problem cost function % n grid samples % x_min minimum value of x range % x_max maximum value of x range % y_min minimum va...
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MATLAB
1,560
53
% Sample nested object to test expandable properties. % Copyright 2008-2009 Levente Hunyadi classdef SampleNestedObject properties RealDoubleScalar = pi; RealDoubleRow = [1.5,2.5,3.5,4.5]; RealDoubleColumn = [1.5;2.5;3.5;4.5]; RealDoubleMatrix = [1.5,2.5;3.5,4.5]; R...
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MATLAB
1,561
54
function [beta, mse, Rs, eps] = regress_Y_on_X(Y, X, random_inter, groups) % Perform multiple regressions using \ and return key metrics. % Y = X*beta % A column of ones is appended to X to add an intercept term. % % Inputs: % - Y: (N,M) matrix, where % N = nb of observations and % M = nb of ...
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MATLAB
1,561
50
function [params, precomputedPortion] = scaleWB3(params, spkHistPrior_setup, couplingGroup) % i.i.d non-mean Gaussian over spike history coefficients & constant K = size(params.B,1); w_mu_idx = 1; w_sig_idx = 2; H = double(params.H); w_mu = H(w_mu_idx); log_w_sig = H(w_sig_idx); w = double(params.W); precomput...
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MATLAB
1,561
60
% 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 Figure 3 - figure supplement 1d clear all; close all; clc; % Load estimates generated from gLME ...
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MATLAB
1,562
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function meandist = meandist_estim(data, use_data) % UltraMegaSort2000 by Hill DN, Mehta SB, & Kleinfeld D - 07/09/2010 % % meandist_estim - Estimate the average distance between vectors. % % Usage: % meandist = meandist_estim(data, use_data) % % Description: % MEANDIST = MEANDIST_ESTIM(DATA) takes an (M x N) mat...
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MATLAB
1,564
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function [EEG,data_sd]=chan_variance(EEG,varargin) g=struct(varargin{:}); try g.data_field; catch, g.data_field='data'; end; if strcmp(g.data_field,'data'); try g.chan_inds; catch, g.chan_inds=1:EEG.nbchan; end; else try g.chan_inds; catch, g.chan_inds=1:size(EEG.icawinv,2); end; end try g.epoch_inds; ...
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MATLAB
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function handles = updateTrialHistoryPassive_SanesLab(handles,variables) %handles = updateTrialHistory_SanesLab(handles,variables) % %Custom function for SanesLab epsych % %This function updates the GUI Trial History Table. % %Inputs: % handles: GUI handles structure % variables: matrix of trial information % % % ...
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MATLAB
1,565
43
% PURPOSE: creates a figure for an ERPLAB Studio window or dialog. % % FORMAT: % % h = f_estudio_figure(...) % % Takes and returns exactly what figure() does. The only difference is that the % figure carries pixel font units as a default, so every component built inside % it reads its FontSize in pixels rather than poi...
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MATLAB
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50
function tbadd(table,names,types,varargin) % tbadd Create MySQL table [mym utilities] % Inputs table - table name, string % names - column-name list, (m*1) cell array % types - column-type list, (m*1) cell array % over - string 'replace' to allow overwrites (optional) ...
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MATLAB
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42
%%This code extract features from kinematics; please follow the example_kinematics.mat file for data preparation %%Created by Xianghao 03/02/2021 Dir_code = ''; %Please fill in the code directory with: extract_fft.m Dir_kinematics = ''; %Please fill in the directory of kinematics. dataset = ''; %Name the output...
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MATLAB
1,571
55
function [dz_values, Nz] = set_up_dz(G) % Set up adaptive mesh increase_factor = G.increase_factor_z; G.Na_channel_start_z = (G.Na_channel_end_z+G.Na_channel_start_z)/2 - 1; G.Na_channel_end_z = G.Na_channel_start_z + 2; G.K_channel_start_z = (G.K_channel_end_z+G.K_channel_start_z)/2 - 1; G.K_channel_end_z = G.K_chan...
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MATLAB
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52
function [windowed, windowedF, MemSpan, MemSpanF, leaky_int, leakyF_int, ... MemDecay, MemDecayF, Weight, Gaussian] = get_memParams(param) % Extract the memory params from the input argument. % % From CountEventInMemory.m. % Used in MarkovNoJump.m, CountEventInMemory.m % Dounia Mulders -- 2019. windowed = 0;...
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MATLAB
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function conf = set_conf() confFile = fullfile(userpath, 'hen_conf.mat'); if exist(confFile, 'file') load(confFile, 'conf'); end if ~exist('conf', 'var') conf = struct(); end if ~isfield(conf, 'dataDir') conf.dataDir = fullfile(getenv('USERPROFILE')); end if ~isfield(conf, 'solutionsDir') ...
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MATLAB
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51
function [hFigsSorted] = sortfighandlearray(hFigs,varargin) %SORTFIGHANDLEARRAY Due to changes in Matlab 2014b graphics system, figure %handles are no longer doubles, but rather an graphics object. Hence, these %objects can not be sorted directly. This function accepts an array of %figure handles, and returns an array ...
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MATLAB
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40
function chargeForPercep = charge_for_num_fibers(nerveModel, electrodeType, placements, numAS, numFibersForPercep) %CHARGE_FOR_NUM_FIBERS Summary of this function goes here % Detailed explanation goes here paramSet = '1'; chargeForPercep = zeros(numel(placements), numAS); for iPlacement = 1:numel(placements)...
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MATLAB
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40
%Code by Paolo Velásquez - YachayTech University %Biomedical Engineer Student. %School of Biological Sciences and Engineering. imds = imageDatastore('ImageData5', ... 'IncludeSubfolders',true, ... 'LabelSource','foldernames'); %auimds = augmentedImageDatastore(imds,'ColorPreprocessing','gray2rgb'); [im...
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MATLAB
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clear all; % Add decoding functions to path addpath('../'); %% 1. 2class problem %% 1.1. Generate data % Specificy parameters numF = 2; numN0 = 50; numN1 = 150; m0_true = [0 1]'; % True mean for class A m1_true = [0 -1]'; % True mean for class B S0_true = [1 .6; .6 1]; % True covaria...
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MATLAB
1,578
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function hfig = plotSpectra(signal,fs,fmin,fmax,dim) % PLOTSPECTRA plots the Fourier spectrum and and wavelet spectrogram of % input signal SIGNAL with sampling frequency FS. Spectra are computed % between minimum frequency FMIN (default 1 Hz) and maximum frequency FMAX % (default 100 Hz). Signal is assumed to be in th...
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MATLAB
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function [y,t2] = ode45_Liley(t, params) % simulate deterministic version of the Liley model using ODE45 he_rest=params(1); hi_rest=params(2); Nee_beta=params(3); Nei_beta=params(4); Nie_beta=params(5); Nii_beta=params(6); Gamma_e=params(7); Gamma_i=params(8); gamma_e=params(9); gamma_i=params(10); Tau_e=params(11); T...
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MATLAB
1,580
51
function localDataPath = setLocalDataPath(varargin) % function LocalDataPath = setLocalDataPath(varargin) % Return the path to the root CCEP directory and add paths in this repo % % input: % personalDataPath: optional, set to 1 if adding personalDataPath % % when adding personalDataPath, the following function sho...
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MATLAB
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function [results] = spkHistPrior2(params, results, spkHistPrior_setup, addDPriorForWB) % 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); log_w_sig = H(w_sig_idx); log_b_sig = H(b_sig_idx); %% log hyperprior if(isfield(re...
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MATLAB
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function S = ReadDATags(DA,TRIALS,params) % S = ReadDATags(DA,P) % S = ReadDATags(DA,P,params) % % % Reads current values from an RPvds circuit running on a TDT module into a % structure S. % % P is a Protocol structure (typical a field in the CONFIG % structure) % ex: S = ReadDATags(DA,CONFIG(1).PROTOCO...
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MATLAB
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function status = GetFeatureIndices(self) streams = self.ConfigFile.GetParams('Streams'); cams = self.ConfigFile.GetParams('CameraNames'); videoNames = GetVideoNames(self); if self.VerboseLevel > 0 fprintf(' Collecting feature status for %d videos ', length(videoNames)) end Video = {}; FeatureIndices = {}; f...
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MATLAB
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function [y] = my_sub_sep_icwt(P, f, f_span) % this sub-function is used to reconsturct the signal from the wavelet transform (the wavelet basis is selected as the type proposed By Tognola) % fprintf('Calculating ICWT ... ') % 'x' - the original data samples % 'f' - the discrete frequency samples (normalized) ...
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MATLAB
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function handles = TrialDelivery_Callback_SanesLab(handles,status) %handles = TrialDelivery_Callback_SanesLab(handles,status) % %Custom function for SanesLab epsych % %This function turns trial delivery on or off when the DELIVER TRIALS or %PAUSE TRIALS button is pressed, respectively. % %Input: % handles: GUI handl...
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MATLAB
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function plotLinFit(X,Y,yfit,P,Powers,Rsq,xlabl,ylabl) % Plots data and their polynomial fits. Figure title includes polynomial % coefficients and r-square % %__________________________________________________________________________ % Copyright (C) 2022 Laboratory for Neuroimaging Research % Written by A. Lutti,...
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MATLAB
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function cov = plotEigenspectra(r,compDimP,sideTransec) %%% This function will plot the eigenspectra cov = squeeze(nanmean(r.Cov_comp ./ nansum(r.Cov_comp,[1 4]),2))*100; figure('Position',[680 380 500 330]); for f = 1:numel(compDimP.focusOnList) focusOn = compDimP.focusOnList{f}...
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MATLAB
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function demo_lasso_cv() % demonstration file for SparseGDLibrary. % % This file illustrates how to use this library in case of problems with % trace norm minimization. % % This file is part of SparseGDLibrary. % % Created by H.Kasai on June. 01, 2017 clc; clear; close all; %% prepare datas...
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MATLAB
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function Val = ArduinoCom(A,Command,timeout) % Val = ArduinoCom(A,Command) % Val = ArduinoCom(Command) % Val = ArduinoCom(...,timeout) % ArduinoCom(...,Command,...) % % A ... Serial object (required on first call) % Command ... command string % timeout ... define timeout duration when waiting for a response from...
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MATLAB
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function [RICAModel, path] = LoadRICAModel(self) %LOADRICAMODEL Load dimensionality reduction model if it exists % [RICAMODEL, PATH] = LOADRICAMODEL(SELF) loads rica model for STREAMS, % CAMERANAMES, and NUMDIMENSIONS specified in config file if it exists. % % If model exists, returns ReconstructionICA object R...
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MATLAB
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function [Drift] = DriftData(patient) Drift = []; DriftControl = []; numberConditions = 2; filename = strcat('Patient', int2str(patient), '/Patient', int2str(patient), 'DriftPosition.txt'); delimiterIn = ' '; headerlinesIn_control = [4, 8, 12, 16, 20, 24]; % headerlinesI...
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MATLAB
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function lat = compare(lat,P) lat = calc_pi(lat, P, @Imin); PImin = lat.PI; arr = sprintf('%6.4f ',PImin); fprintf(1,'PI with Imin: [ %s ]\n',arr); if lat.Nx==3 display_nonzero_terms(lat) end % lat = calc_pi_ri(lat, P, @Iccs); % PIccs = lat.PI; % arr = sprintf('%6.4f ',PIccs); % fprintf(1,'PI with Iccs: [ %...
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MATLAB
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function model = dtipm_pipe_SDPdSL(data,btensors,D0,mask,nvox,ind,parallel,cvxsolver) % function model = dtipm_pipe_SDPdSL() % % reshape data and retain voxels within the mask siz = size(data); data = reshape(data, prod(siz(1:3)), siz(4))'; mask = reshape(mask, prod(siz(1:3)),1)'; si = find((mask>0).*(~all(data==0,1))...
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MATLAB
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function dbs = DB_Connect(host,user,pass) % dbs = DB_Connect % dbs = DB_Connect(host,user,pass) % dbs = DB_Connect(forcePrompt) % % Connect to database via mym % % Returns list of databases if successful connection is established % % DJS 2013 prevcon = getpref('DB_Connect',{'host','user','pass'},{'','',''})...
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MATLAB
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function findLocalDistance() thisValues = pdist2(currentStream(calcIndex,:), currentStream); smoothSigma = 1; x = -ceil(3*smoothSigma):ceil(3*smoothSigma); kernel = -x.*exp(-x.^2/(2*smoothSigma^2))/(smoothSigma^3*sqrt(2*pi)); currentDiff = filterData(currentStream, 0, kernel, 1, 0); thisDiffDi...
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MATLAB
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function tp_analyzeallRAW(prefix, depth) % TP_ANALYZEALLRAW - Traverse all tp 'stack' folders for a given experiment, click analyze raw, and add to database % % TP_ANALYZEALLRAW(PREFIX, [DEPTH]) % % Given a data directory in PREFIX, explore all subdirectories to identify which are % VH Lab experiment directories (with...
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MATLAB
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function model = qtipm_pipe_SDPdcSL(data,btensors,D0,mask,nvox,ind,parallel,cvxsolver) % function model = qtipm_pipe_SDPdcSL() % % reshape data and retain voxels within the mask siz = size(data); data = reshape(data, prod(siz(1:3)), siz(4))'; mask = reshape(mask, prod(siz(1:3)),1)'; si = find((mask>0).*(~all(data==0,1...
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MATLAB
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function edl = eda_edl(eda, fs, t) % EDA_EDL Measure Electrodermal Level (EDL). % edl = EDA_EDL(eda, fs, t) % % Input arguments: % eda - 1-by-n vector of EDA samples % fs - sampling rate (Hz) % t - 2-by-k matrix of k time intervals % % Output arguments: % edl.v - 1-by-k vector of measured EDL d...
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MATLAB
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function [chan_order, order_desired] = define_chan_order_colors(chanlocs, desired_chans) % Return the indices to use to obtain the channels in the order specified % by desired_chans. % The channels that are specified in desired_chans but cannot be found in % chanlocs are ignored. % % Out % chan_order idx of ...
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MATLAB
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function [loo,loos,pk] = psisloo(log_lik) %PSISLOO Pareto smoothed importance sampling leave-one-out log predictive densities % % Description % [LOO,LOOS,KS] = PSISLOO(LOG_LIK) computes Pareto smoothed importance % sampling leave-one-out log predictive densities given posterior % samples of the log likelih...
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MATLAB
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function ax = make_axes_on_grid( axes_pos, params, h, visibility) % UltraMegaSort2000 by Hill DN, Mehta SB, & Kleinfeld D - 07/12/2010 % % make_axes_on_grid - returns axes object with specified position % % Usage: % ax = make_axes_on_grid( axes_pos, params, h, visibility) % % Description: % This is a utility fun...
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MATLAB
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function Subregions=getROIpairs(TissueType) % Computes pairs of regional atlas labels extracted from the left & right hemispheres. % % INPUTS: % - TissueType: tissue class of interest for the extraction of the atlas labels. Possible values: 'WM' (white % matter, 'GM' (grey matter) or 'GMnoB0' (grey matter afte...
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MATLAB
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function plot_selectivity(model, Q) if ~exist('Q', 'var') Q = linspace(0, get_max_threshold(model)); end [fascIdsByAs, activeSites] = load_active_sites(model.paths); elecIds = unique([activeSites.elecId]); separateElectrodes = numel(elecIds) > 1; % Choose a color per fascicle colorset = distinguishabl...
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MATLAB
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clc close all clear variables %date:6th Feb 2021 %VM font = 14; linewidth = 2; format long; %addpath('/Users/varunmannam/Desktop/Spring21/Research_S21/Feb21/SPIE_SR/old_SR_files/mse_plots/'); addpath('/Users/varunmannam/Desktop/Spring21/Research_S21/Feb21/0702/SR_new_results/mse_loss/'); %new simulations lr1 = load('...
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MATLAB
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clc close all clear variables %date: 6th Feb 2021 %VM font = 14; linewidth = 2; format long; %addpath('/Users/varunmannam/Desktop/Spring21/Research_S21/Feb21/SPIE_SR/old_SR_files/mse_plots/'); addpath('/Users/varunmannam/Desktop/Spring21/Research_S21/Feb21/0702/SR_new_results/mse_loss/'); %new simulations lr1 = load(...
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MATLAB
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function associate_Beh_epData_files(subject) pn = fullfile('/Users/kpenikis/Documents/SanesLab/Data/raw_data',subject); pnB = fullfile(pn,'BehaviorData'); epData=[]; Beh_files = dir(fullfile(pnB,'old','*.mat')); for ii = 1:numel(Beh_files) load( fullfile(pnB,'old', Beh_files(ii).name) ); disp(Beh_f...
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MATLAB
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% ciplot(lower,upper) % ciplot(lower,upper,x) % ciplot(lower,upper,x,colour) % % Plots a shaded region on a graph between specified lower and upper confidence intervals (L and U). % L and U must be vectors of the same length. % Uses the 'fill' function, not 'area'. Therefore multiple shaded plots % can be overlayed wit...
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MATLAB
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function [cn,err,R] = f_CN_smp(CIJ,maxSamp) % Approximation of CN using "sampling method" % FC is computed using Galan's linear model % References % L. Barnett, C. L. Buckley and S. Bullock (2009) % % R. F. Galan, plos one (2008) if nargin < 2 maxSamp = 500; end N = size(CI...
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MATLAB
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function [rEnergy, f, t] = AD_MP_Ass(data,params) % Temporary workspace for MP decomposition folderName = ['/Users/aleksanderdomanski/Documents/MATLAB/MPtest' '/data/']; tag = 'test/'; Max_iterations = 1000; % number of iterations % Import the data L_orig = size(data,1); % Unpadded signal length L = 2^nex...
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MATLAB
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function ParseVarargin(paramkeys,varnames,vin) % ParseVarargin(paramkeys,varnames,vin); % % Single line 'varargin' checking. 'vin' should be the varargin cell % array for the calling functiion. % % ParseVarargin(paramkeys,[],vin) will use the paramkeys value as a % variable name. Note: spaces are invalid in ...
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MATLAB
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function A = ArduinoConnect(varargin) % A = ArduinoConnect % % Connect to a USB Arduino microcontroller. % % This function waits for the Arduino to print the character "R" to the % serial bus. % % BaudRate ... Connection baud rate (default = 57600) % aName ... Connection name (default = 'Arduino...
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MATLAB
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%% This is example of usage of model. However you can use anything more complex or even simpler. model_version_id = 4; fitted_parameters = [1, 2, 1.1, 0.9, 0.3, 12, 5, 0.9]; % Fitted parameters order: h, k, c, w, w_E, sigma_H, sigma_E, d_f % fitted_parameter_names = {'h', 'k', 'c', 'w', 'w_E', 'sigma_H', 'sigma_E...
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MATLAB
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function model = dtip_data2fit_NLLSd(model,signal,bten,ind) % function m = dtip_data2fit_NLLSd(model,signal,bten,ind) % % fits the DTI parameters using NLLSd if (nargin < 4), ind = ones(size(bten,1),1)>0; end signal = signal(ind); bten = bten(ind,:); model = double(model); % convert between fit and SI units SI_to_fi...
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MATLAB
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function C = findConsecutive(ind,N,g) % C = findConsecutive(y) % C = findConsecutive(y,N) % C = findConsecutive(y,N,g) % % Find consecutive values in a vector. % % Inputs: % ind logical vector % N minimum number of consecutive ones to find in y (default = 2) % g forgive a maximum of g ...
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MATLAB
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function lme_lowessPlot(time,y,bw,group) % lme_lowessPlot(time,y,bw,group) % % Time plot of the lowess regression curve estimating the trend in the % mean response over time (Depends on the curve fitting toolbox). % % Input % time: Time covariate (ordered according to time for each subject) . % y: Ordered data vector (...
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MATLAB
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function analyzetpstack_analyzerawfromlist(prefix, experlist, stacknamelist, channellist) % ANALYZETPSTACK_ANALYZERAWFROMLIST - Analyze raw F from a list of analyzetpstack stacks % % ANALYZETPSTACK_ANALYZERAWFROMLIST(PREFIX, EXPERLIST, STACKNAMELIST, CHANNELLIST) % % Analyzes a set of experiments. First, the progr...
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MATLAB
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function [nfigs,fighandles]=figs_to_ps(filename,newFileFlag, paper_orientation,volubleFlag) % [nfigs,fighandles]=figs_to_ps(filename,paper_orientation,volubleFlag) % prints all figures to output.ps % % nfigs: number of figures printed % newfileflag: flag to make new .ps file or append existing file % fighand...
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MATLAB
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function varargout = gen_logchirp(Fs,t1,f,phi,gate_dur) % [y,<t>] = gen_logchirp(Fs,t1,f,<phi>,<gate_dur>) % % Produce logarithmic swept-sine. % % Input: % Fs ... Sampling frequency (Hz) % t1 ... Duration of sweep (seconds) % f ... Frequency range of sweep (Hz), ex: [100 10000] % phi ...
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MATLAB
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function [in] = get_default_IO_in() % Return default inputs for the IdealObserver code. MemParam = {'Decay', [8]} ; AboutFirst = 'WithoutFirst' ; learned_param = 'transition' ; %'transition' ; % 'frequency', 'transition', 'alternation' in.learned = learned_param ; % estimate TPs in....
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MATLAB
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function S = cooling_perm_test(nX, nY, correctX, correctY) % % This test calculates the difference in proportion correct between % conditions X (e.g. control) and Y (e.g. cooled) % % nX, nY = number of trials overall % correctX, correctY = number of trials correct % Options nIterations = 1e4; draw = false; % Allows vi...
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MATLAB
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function grid = vector2grid(vector) % Converts a 1x100, 100x1 or 100xt vector into a 10x10 or 10x10xt grid, % rotated correctly. channelDim optionally specifies the dimension % specifying channel number, which must have length 100. % % NOTE: THIS TRANSFORMATION CHANGES THE INDEXING OF THE DATA % A row vector is stored ...
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MATLAB
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function matrix= get_pce_matrix_noise_average(res_list, cluster_list_with_image_idx, dir, iter, img_dim) % This function compute PCE matrix which includes pairwise PCE correlation among all noise residuals (before merging/clustering). % INPUT: % res_list A list of residual paths % cluster_list_with_image_idx ...
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MATLAB
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function getStats(S, options) % Get number of masks masks = unique(S.Mask); nMask = numel(masks); % For each mask for i = 1 : nMask % Filter for mask rows = S.Mask == masks(i); T = S(rows,:); % Calculate average temperature T.Temperature = mean([T.LeftTemperature T.RightTemperature],...
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MATLAB
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% Help text associated with a function, class, property or method. % Spaces are removed as necessary. % % See also: helpdialog % Copyright 2008-2010 Levente Hunyadi function text = helptext(obj) if ischar(obj) text = gethelptext(obj); else text = gethelptext(class(obj)); end text = texttrim(text)...
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MATLAB
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%% Setup % This script writes CSV files for the chord diagram in R % Note: the tastes are combined now util.clearAll; % stimuli cur_save_dir = fullfile(util.get_paths().figs,'CSV_modules'); util.mkdir(cur_save_dir) %% Write the CSV files for chord diagram (R) regions = {'PFC', 'OFC', 'ACC_area24', 'agranularIns_bin',...
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MATLAB
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function pvpmod(x) % PVPMOD - evaluate parameter/value pairs % pvpmod(x), where x is a cell array with an even number of cells, assigns % the value x(i+1) to the parameter defined by the string x(i) in the % calling workspace. This is useful to evaluate <varargin> contents in an % mfile, e.g. to change def...
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MATLAB
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function out_array=marks_label2index(marks_struct,labels,out_type,varargin) %% INITIATE VARARGIN STRUCTURES... try options = varargin; for index = 1:length(options) if iscell(options{index}) && ~iscell(options{index}{1}), options{index} = { options{index} }; end; end; if ~isempty( varargin ), g...
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MATLAB
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function [output] = ERBFilterBank(x, fcoefs) % function output = ERBFilterBank(x, fcoefs) % Process an input waveform with a gammatone filter bank. Design the % fcoefs parameter, which completely specifies the Gammatone filterbank, % with the MakeERBFilters function. % % This function takes a single sound vector, and ...
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MATLAB
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function updatepump_SanesLab(handles) %updatepump_SanesLab(handles) % %Custom function for SanesLab epsych % %This function sets the pump rate using flow rate specified in the GUI % %Inputs: % handles: GUI handles structure % % %Written by ML Caras 7.25.2016. Updated 8.22.2016. global PUMPHANDLE GUI_HANDLES AX RUNT...
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MATLAB
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function ds_info=my_gen_ds_info_hof(ds_config) ds_dir=fullfile('../datasets', 'hof'); train_idx_file=fullfile(ds_dir, 'ImageSets/Segmentation/train.txt'); fid=fopen(train_idx_file); train_file_names=textscan(fid, '%s'); train_file_names=train_file_names{1}; fclose(fid); val_idx_file=fullfile(ds_dir, 'ImageSets...
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MATLAB
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%This script allows to transform Z maps from Activation Likelihood %Estimation analysis into minimum Bayes Factor maps. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %fin= a Z map obtained through a p-to-Z conversion from a p-value map, as it is produced at the end of any Activation % Like...
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MATLAB
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function ds_info=my_gen_ds_info_eyth(ds_config) ds_dir=fullfile('../datasets', 'eyth'); train_idx_file=fullfile(ds_dir, 'ImageSets/Segmentation/train.txt'); fid=fopen(train_idx_file); train_file_names=textscan(fid, '%s'); train_file_names=train_file_names{1}; fclose(fid); val_idx_file=fullfile(ds_dir, 'ImageSe...
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MATLAB
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function ds_info=my_gen_ds_info_gtea(ds_config) ds_dir=fullfile('../datasets', 'gtea'); train_idx_file=fullfile(ds_dir, 'ImageSets/Segmentation/train.txt'); fid=fopen(train_idx_file); train_file_names=textscan(fid, '%s'); train_file_names=train_file_names{1}; fclose(fid); val_idx_file=fullfile(ds_dir, 'ImageSe...
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MATLAB
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function queryVal = GetParams(self, varargin) % queryValStruct = GetParams(self, 'project') % queryVal = GetParams(self, 'CameraNames') % queryVal = GetParams(self, 'project', 'CameraNames') self = GenerateParams(self); params = self.Params; if nargin == 3 section = varargin{1}; query = varargin{2}; quer...
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MATLAB
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function Q = S_object(prediction,GT) % S_object Computes the object similarity between foreground maps and ground % truth(as proposed in "Structure-measure:A new way to evaluate foreground % maps" [Deng-Ping Fan et. al - ICCV 2017]) % Usage: % Q = S_object(prediction,GT) % Input: % prediction - Binary/Non binary f...
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MATLAB
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%%This function is to compute the specific time-range for xth columns for %%Overlay setting function [bindatadjust,Xtimerangeadjust,Xticksadjust,TimeAdjustOut,XtimerangeadjustALL] = f_adjustdata_xyrange_xyticks_overlay(bindatatrs,Xtimerange,qXticks,offset,NumColumns,PosIndexs,stepXP) bindatadjust = []; Xtimerangea...
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MATLAB
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%----------------------------------------------------------------------- % Job saved on 07-May-2022 10:01:08 by cfg_util (rev $Rev: 7345 $) % spm SPM - SPM12 (7771) % cfg_basicio BasicIO - Unknown %----------------------------------------------------------------------- clear matlabbatch subjfolder = dir('F:\fMRI_QC\fm...
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MATLAB
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function [messgStr,viewerpanelIndex ]= f_check_erpviewerpanelchanges() messgStr = ''; viewerpanelIndex = 0; MyViewer_ERPset = estudioworkingmemory('MyViewer_ERPsetpanel'); if ~isempty(MyViewer_ERPset) && MyViewer_ERPset==1 messgStr = char( 'Changes on "ERPsets" have not been applied'); viewerpanelIndex =1; ...
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MATLAB
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%===================================================== % FileName: extract_online_tiletraces.m % Designby: Zhe % Modified: 07/08/2021 % Describe: Extract fluorescence traces from the calcium image dataset. % Suppose C: Number of tiles; T: Number of frames % traces <C,T> %===========================...
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MATLAB
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function ds_info=my_gen_ds_info_egohands(ds_config) ds_dir=fullfile('../datasets', 'EgoHands'); train_idx_file=fullfile(ds_dir, 'ImageSets/Segmentation/train.txt'); fid=fopen(train_idx_file); train_file_names=textscan(fid, '%s'); train_file_names=train_file_names{1}; fclose(fid); val_idx_file=fullfile(ds_dir, ...
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MATLAB
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function [GlobalScores, ClassScores] = ScoreClips(clipT) % groundTruthLabels = vertcat(clipT.Prediction{:}); groundTruthLabels = []; methodLabels = []; for i=1:size(clipT, 1) groundTruthLabels = [groundTruthLabels; clipT.Annotations{i}.Label]; methodLabels = [methodLabels; clipT.Annotations{i}.Prediction]; ...
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MATLAB
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function visualiseState( V, Nx, Ny, occ_map, t ) % This function visualises the membrane potential map % Internal flag specifies whether to visualise as 'surfaces' or points vis_surfaces = false; % Convert vector V back into a matrix (use transpose for correct % orientation because reshape works 'columnwise') V = res...
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MATLAB
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function [counts,x_inds,y_inds] = histxy(x, y, D, filt) % UltraMegaSort2000 by Hill DN, Mehta SB, & Kleinfeld D - 07/12/2010 % % histxy - 2D histogram of joint x and y values % % Usage: % [counts,x_inds,y_inds] = histxy(x, y, D, filt) % % Description: % Returns a matrix containing counts for how many data points...
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MATLAB
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function S = ReadRPTags(RP,TRIALS,params) % S = ReadRPTags(RP,TRIALS) % S = ReadRPTags(RP,TRIALS,params) % % % Reads current values from an RPvds circuit running on a TDT module into a % structure S. % % C is a single index the configuration structure % ex: S = ReadRPtags(RP,C(2)); % % RP is a handle (...
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MATLAB
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function [files, exists] = GetValidFolderFiles(parentFolder, varargin) p = inputParser; addOptional(p, 'Contains', ''); addOptional(p, 'DoesNotContain', ''); addOptional(p, 'Extension', ''); parse(p, varargin{:}); d = dir(parentFolder); dfolders = d(~[d(:).isdir]); if isempty(dfolders) files = []; exists = f...
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MATLAB
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function reformat_tank_data_jy(BLKS) %reformat_tank_data % Function to reformat and save ephys data from epsych program. % % Program prompts user to select TANK, then cycles through each BLOCK, % calls TDT2mat (@DJS) to reformat tank data to a matlab struct, then % saves as a -mat file in google drive folde...
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MATLAB
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% Collect interim single cell data from KDE convert code into HP and PFC archives % No event times pass through this version % Aleksander PF Domanski PhD UoB 2015 % aleks.domanski@bristol.ac.uk % % You need to run this after big batch jobs on Blue Crystal to gather all % individually saved single unit files into...
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MATLAB
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%% Setup util.clearAll; outdir = fullfile(util.get_paths().figs,'graph_centrality'); util.mkdir(outdir) %% Setup graph % Read beta values and calculate their correlation beta_tables_taste = util.load.all_taste_betas(); % first read the full matrix avg_corr = connect.correlations(beta_tables_taste.combined, ... {{'...
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MATLAB
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function params = setPatternParams(Fs) % Function to set parameters for pattern detection, given sampling % frequency Fs (in Hz) % Minimum order parameter for a plane wave to be detected planeWaveThreshold = 0.85; %planeWaveThreshold = []; % Maximum velocity field magnitude for synchrony to be detected synchronyThresh...
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MATLAB
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function reformat_tank_data_kp(BLKS) %reformat_tank_data % Function to reformat and save ephys data from epsych program. % % Program prompts user to select TANK, then cycles through each BLOCK, % calls TDT2mat (@DJS) to reformat tank data to a matlab struct, then % saves as a -mat file in google drive folde...