sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9a6faf7964239e6888219bccee77061bfeae012c555932a2d60e3d5085541009 | MATLAB | 2,039 | 105 | %% plotVisTime
% clear; close all; clc
%% Initialize parameters
start = 1;
stop = -1;
stop = 98;
plotOn = 0;
rollOn = 0;
stDay = 1;
params = struct();
% set day 1 params
params(1).buffSt = 2.5;
params(1).buffEnd = 0.5;
params(1).timeCue = 5;
% set day 2 params
params(2).buffSt = 1;
params(... |
caf29f18c135b292b6279e128278333aaedc2a92bee9491e2cff260b69e0d84c | MATLAB | 2,041 | 48 | function varargout = check_ch(self, channels, checkType, varargin)
%check_ch - Check that the appropriate channels are present
%
% check_ch(OBJ, CHS, 'any') checks that at least one of the channels
% specified by CHS are present in OBJ. CHS must be a single row char
% array or a cell array containing single row ... |
4f3594b12002af7b465251d04a99cc7e74349fcfe0846bacab822a60a42bb444 | MATLAB | 2,042 | 72 | % Causal diagrams
clear; clc
N = 10*10^3;
nvartot = 5;
addpath("~/gdrive/Dottorato_Matlab/ToolBox/robince-gcmi/matlab/")
%% COLLIDER : 2 --> 1 && 3 --> 1 (SYNERGY)
X = randn(N,nvartot);
X(:,1) = 0.8*X(:,2) + 0.3*X(:,3) + 0.15*randn(N,1);
out = goi_gradients(X,nvartot);
fprintf("COLLIDER: 2 --> 1 && 3 --> ... |
531f629412a03707d6d35462531503805bb831d1d159f0554215047a1e440bed | MATLAB | 2,043 | 64 | %% Motion Correction
% Motion correction is designed to correct for motion artefacts in the raw
% images that often result from movement of the sample. This may occur
% through microscope drift or movement of the sample (e.g. animal) itself.
%% See Also
% * <matlab:doc('utils.motion_correct') Motion correction utilit... |
f6ec6dee236cf02508401bf3becf23b1075507489389e915020e0d3201c4299c | MATLAB | 2,044 | 90 | function sff = sff_dk(sff)
%SFF_DK
%
% RS, 05/2022
n1 = sff.gp1.cln.n;
n2 = sff.gp2.cln.n;
[dk,dkres] = dkRobust(n1,n2);
sff.clb.dk = dk;
sff.clb.dkres = dkres;
end
function [dk,res] = dkRobust(N1,N2)
%DKROBUST Calculates dk from raw N (number of objects) time series
% Removes outliers due t... |
ba7243134b5a37ec614f22d92079c8210616ab783018368bba6cf09a78cac868 | MATLAB | 2,054 | 67 |
close all force
%
clear
load('a0_0_bhv2trialStrct.mat');
load a19_0_downSizeAverageHeatMaps.mat
load a19_1_calculateGradAveragesForEachConditionAndBaseline.mat
%}
%%
nTrial = numel(dataTrl) ;
NTrial = 1:nTrial;
tAll = tic;
hWB = waitbar(0,'checking the trials ...');
nTrialAllNext = 0;
iTrialAll = 0;
distAll = na... |
7d6c240f6b4bc6ea5d6502bba4593ad3d5624bb74b25afbee5bdbab01cf55398 | MATLAB | 2,057 | 89 | function [uF,uA] = testPointPlace
% Test adding a line that follows the cursor as it goes down.
%
% Clicking adds points. Shift-clicking removes them.
uF = uifigure;
uA = uiaxes('Parent',uF);
uA.DataAspectRatio = [1,1,1]; % Make axis aspect ratio square
pan(uA,'off')
zoom(uA,'off')
... |
cd2e56032cd72567999109f9eecb6114100ca1171d6c93071c493511209f5155 | MATLAB | 2,059 | 81 | clear all
thetaRight = -[67.5 112.5 157.5 157.5 -157.5 -112.5 -112.5 ...
-67.5 -22.5 -22.5 22.5 67.5];
thetaLeft = -[-67.5 -22.5 22.5 22.5 67.5 112.5 112.5 ...
157.5 -157.5 -157.5 -112.5 -67.5];
thetaFB = -((0:30:330) + 15);
% Parameters from data fit
a = 29.2282;
b = 2.1736;... |
0ffc2b47cee086f734eadfba129a610c75be0e87e1c8a72bda1dc3459077c68e | MATLAB | 2,060 | 80 | function y = nanstd(x,dim,flag)
% FORMAT: Y = NANSTD(X,DIM,FLAG)
%
% Standard deviation ignoring NaNs
%
% This function enhances the functionality of NANSTD as distributed in
% the MATLAB Statistics Toolbox and is meant as a replacement (hence the
% identical name).
%
% NANSTD(X,DIM) calculates the st... |
272e85c1f2c79ad1ac632c45997579b14ca32eb07b8e0df44e711599ff06a94a | MATLAB | 2,060 | 50 | function f = LK_PlotFiringRateInOutPlaceField_20231012(dt)
%
% LK_PlotFiringRateInOutPlaceField_20231012 plots the firing rate inside
% vs. outside the place fields (using a boxplot).
%
% Input is a structure with multiple fields.
%
% Output is a figure handle.
%
% Lukas Kunz, 2023
%% groups
% mean and standard error... |
d7ee2f9db2b521f437bfae7d630c783c3a4a38acfd255ce3389353414f6f8030 | MATLAB | 2,060 | 64 | % this code will read all the gaze files from the trials and covernt them
% to the image coordinate.
clear
close all force
warning on
imSize = [733, 977];
pix2deg = 34.910;
hWB = waitbar(0,'checking the trials ...');
%load tirals info
load('a0_0_bhv2trialStrct.mat');
I = arrayfun(@(x) isfield(x.analyze,mfilename),... |
6386d80fbdb511287df63f4910c46b89e28f6b299abb4fba04920d05ebc80e4b | MATLAB | 2,064 | 58 | function process_sub(self, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the Licen... |
9c2713dce4d09b12443f4a380e72028e9deccfe002adcc9c6c9cece1c3ee21d8 | MATLAB | 2,064 | 73 | %%
% Reproduces Fig. 5B and 5C in:
% IA Oldenburg, WD Hendricks, G Handy, K Shamardani, HA Bounds, B Doiron,
% H Adesnik. The logic of recurrent circuits in the primary visual
% cortex. Nature Neuroscience (2024)
%
% Written and edited by G Handy, IA Oldenburg, and WD Hendricks
%%
clear;
% Load the simulation... |
e5683c63e8490151f95a7bcb8a7212cb7f3d2678690b5fe81aa86fc9caeb8615 | MATLAB | 2,066 | 59 | %%
% Recreates the key experimental panels (Figs. 2-4) of the paper:
% IA Oldenburg, WD Hendricks, G Handy, K Shamardani, HA Bounds, B Doiron,
% H Adesnik. The logic of recurrent circuits in the primary visual
% cortex. Nature Neuroscience (2024)
%
% Written and edited by G Handy, IA Oldenburg, and WD Hendricks... |
3436cb88fde397ba0eb13a7fe907f31cfefe618f01d871346b99db535f08bf62 | MATLAB | 2,067 | 68 | function plot_traces(self, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the Licen... |
2731d2ffbc5fc9325223211233d4ceefdef47bd7800a42ce8cdcbebe24e936ca | MATLAB | 2,072 | 65 | function stimLoc = computePosition(display,percCenter,angle,distance)
% return stimloc [percx percy pixx pixy]
% Adjust for angles equal to or greater than 360
divides = floor(angle/360);
angle = angle - (360*divides);
screenDims = [pix2angle(display,display.numPixels(1)) pix2angle(display,displ... |
90dfa22bdbb4289a0efa5c17a939c95015d22d09c3456fb25e876214c0cd3b75 | MATLAB | 2,073 | 57 | function [All] = calcOffTargetRisk(All,opts)
thisPlaneTolerance = opts.thisPlaneTolerance;
onePlaneTolerance = opts.onePlaneTolerance;
numExps = numel(All);
for ind =1:numExps
%%offtargetRisk
stimCoM = All(ind).out.exp.stimCoM;
numCells = size(All(ind).out.exp.allData,1);
allCoM = All(ind).out.exp.all... |
005284169655dc302c95e0d6d476acb68e3575e8efab531c9adb27e4dc30b6b6 | MATLAB | 2,074 | 74 | classdef Mock_ProcessedImg < ProcessedImg & IMock
%MOCK_PROCESSEDIMG Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
properties
calcMock = Mock_Calc();
end
% -------------------------... |
0d6b0bff2fd121d5ce0e5315aebf584d119017ddecfe99b8c9d6768587325b94 | MATLAB | 2,080 | 67 | classdef laser_power_tests < matlab.unittest.TestCase
% These tests ensure that future changes to the code will not alter the laser power calcs
%
%
properties
hZP = []; % Class instance will go here
chanSamples % The pre-computed data
configDir = './laser_power/'; %use setting... |
128affa16568cec965a4ee1691fa5d58387984465e6548a14d0affcaef8005f4 | MATLAB | 2,080 | 61 | function self = choose_acq(self)
%choose_acq - Protected class method allowing the user to manually
% specify/create the acq structure
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU Ge... |
53902d973edc791a6194357a76486324d39ac21ac4768dd7cd9f03c5aaa54748 | MATLAB | 2,084 | 56 | function im = returnCurrentFrame(obj,nFrames)
% Return the last recorded camera image and optionally the last n frames
%
% function im = zapit.pointer.returnCurrentFrame(nFrames)
%
% Purpose
% Return the last frame and, if requested, the last n frames.
%
% Inputs
% nFrames - [optiona... |
cf713f08e183cec754c742af60bbbf861e2f66cb8d09edaf528cb0c8fed09023 | MATLAB | 2,087 | 69 | function CellsortPlotPCspectrum(imgSeq, CovEvals, PCuse)
% CellsortPlotPCspectrum(fn, CovEvals, PCuse)
%
% Plot the principal component (PC) spectrum and compare with the
% corresponding random-matrix noise floor
%
% Inputs:
% imgSeq - input image sequence
% CovEvals - eigenvalues of the covariance matrix
% PCuse... |
9e1678549dd51552aaa95670c79b8d752393d12e2e73034a492f66ecfa7ef8ff | MATLAB | 2,089 | 59 | classdef Test_CalcFindROIsCellSort < matlab.unittest.TestCase
%Test_CalcFindROIsCellSort Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
methods (Test)
function testNoROIs(self)
... |
aff89bac0cfaabf783e49ef622cd1100e05591cb07e0a47dca10e17686aa38e3 | MATLAB | 2,091 | 61 | function adjImgData = adj_traj_delay(delayTime, imgData, pixelTime, ...
xChannel, yChannel)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% ... |
af10e3a261f448ed41936e9a5ade4b6129b3405fe750c7f2fa1273a45c54032f | MATLAB | 2,093 | 51 | %% Preprocessing
clear all;close all;clc;
opts = delimitedTextImportOptions("NumVariables", 9);
opts.DataLines = [1, Inf];
opts.Delimiter = ",";
opts.VariableNames = ["Var1", "VarName2", "VarName3", "VarName4", "VarName5", "VarName6", "VarName7", "VarName8", "VarName9"];
opts.SelectedVariableNames = ["VarName2", "VarNa... |
59c6390ad76bd6d124fb2b919b91022412f4410a5f752badac00cdaf6b773cdc | MATLAB | 2,096 | 66 | %%% baseline_plot.m
%%% Omkar N. Athavale, May 2023
%%% Run and plot simulation for an extended duration (300 s) with no
%%% stimulation
addpath('../matlab_common/')
% run simulation
[t, s, a] = ICC_SMC_Neuro([0 0 0 0 0], [1 1 1], 0, 0, [0 300000]);
T = a(:, 7);
Vm_ICC = s(:,3);
Vm_SMC = s(:,1);
%% quantify varia... |
24544189cc96b75f09c27f0dffa15b4a68a330bfa94c6cf16247113eb35b9bd7 | MATLAB | 2,097 | 64 | %%% aligned_event_plot.m
%%% Omkar N. Athavale, May 2023
%%% Plots a single event with aligned start times but peak rising derivative
%%% across a configurable sweep of parameter values. Default config is for panels of manuscript
%%% Figure 2B.
addpath('../matlab_common/')
names = {'k_{iAno1}', 'k_{iNSCC}', 'k_{iCa50... |
c32150da8d1acb444d3f32d137ab275c0b4faad693edd501606b6e42c7b32a34 | MATLAB | 2,097 | 47 | function f = LK_PlotPowSpectrogramDuringHCRipples_20231005(dt)
%
% LK_PlotPowSpectrogramDuringHCRipples_20231005 plots power spectrograms
% during hippocampal ripples.
%
% Lukas Kunz, 2023
% create figure
f = figure('units', 'centimeters', 'position', [5, 5, 6, 6], 'Color', [1, 1, 1]);
% depict HC ripples
ax1 = axes(... |
d3bd3bdbfdf2c1afdd2a05684fcc0e6b5e048ab8d5f762d15ca992907073861a | MATLAB | 2,098 | 49 | function cfrdObj = from_ImageJ(varargin)
%from_ImageJ - Load ROIs from ImageJ ZIP-file
%
% OBJ = from_ImageJ() prompts the user to select a ZIP-file
% containing the ImageJ ROIs and will create a
% ConfigFindROIsDummy object using the provided information. By
% using <a href="matlab:help utils.create_ImgJ_mask"... |
b6f9ab11f93bcaf77b6507b8e3d1c725783cdfc0f972ec20ca48c4e3bb768d91 | MATLAB | 2,103 | 79 |
clear
close all force
warning on
imSize = [733, 977];
%load tirals info
load('a0_0_bhv2trialStrct.mat');
I = arrayfun(@(x) isfield(x.analyze,mfilename), dataTrl);
if any(I)
I(I) = arrayfun(@(x) x.analyze.(mfilename) , dataTrl(I));
end
NTrial = find(~I);
nTrial = numel(NTrial);
UMuscimol = unique([dataTrl.iM... |
3a8d922a03bcc00989f98cef63a630c0269ea8c7a3611e16200be70aa8270fb5 | MATLAB | 2,104 | 78 | [sa,X] = network_simulation_beluga.getHeadModel;
folder = fullfile(dataFolder,'simulations','example_embedding');
load(fullfile(folder,'model.mat'));
network = network.rebaseNetwork(folder);
[ids,ts,ei] = network.getprenetwork(network.spikingFile);
cons = csvread(fullfile(folder,'postsynaptic_network','connections.cs... |
a59e14c843a1fb8434d70dc514cd6a7dee2a9abdf8de6f63d3c5324bad07eed6 | MATLAB | 2,104 | 73 | function [channel, result] = sshfrommatlabissue(channel,command)
%SSHFROMMATLAB issues commands to a remote computer from within Matlab
%
% [CONN, RESULT] = SSHFROMMATLABISSUE(CONN,COMMAND)
%
% Inputs:
% CHANNEL is a Java ChannelShell object
% COMMAND
%
% Outputs:
% CHANNEL is the returned Java ChannelShell ... |
9b82983a871e28e26c90830ba53379caa69c2587cfdfac21b5b6272c37c6419e | MATLAB | 2,114 | 74 | % sim_spinecho.m
% Robin Simpson and Jamie Near, 2014.
%
% USAGE:
% out = sim_spinecho(n,sw,Bfield,linewidth,sys,tau)
%
% DESCRIPTION:
% This function simulates a spin-echo experiment with instantaneous RF pulses.
%
% INPUTS:
% n = number of points in fid/spectrum
% sw = desired spectral wi... |
410eb7d03de357c21feba3c3043797d5c6aa9914e5cb67c7ccdf625467c39a4c | MATLAB | 2,115 | 74 | function I = goi_mi_gg(x, y, biascorrect, demeaned)
% MI_GG Mutual information (MI) between two Gaussian variables in bits
% I = mi_gg(x,y) returns the MI between two (possibly multidimensional)
% Gassian variables, x and y, with bias correction.
% If x and/or y are multivariate rows must correspond to sample... |
e03a16cfdac3daa77822321b9246b6f730d75edcc4ced870e4ce2457de1ce41d | MATLAB | 2,117 | 55 | function to_long(self)
%to_long - Convert the images to long format
%
% to_long(OBJ) converts the rawdata of the RawImg object to long format.
% That is, the image lines are rearranged into a single, long image
% frame. This is useful when working with image types that are
% line-based instead of frame-based (... |
d39a6901115f53d47e364e49228d62a2db08ffa49f502ce217f86f55b15573de | MATLAB | 2,119 | 69 | function plot_streaks(self, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the Lice... |
2dd612a8dacf73b93aaff8571ebcd33ea867aa0244c1c910b099943b12915cd4 | MATLAB | 2,120 | 52 | function [ match_vector,distances ] = matchPuncta(puncta_rndA,puncta_rndB,pixels_rndA,pixels_rndB)
%This matches round B to round A, getting the nearest 5 neighbors in terms
%of euclidean distance between centroids
[IDX,D] = knnsearch(puncta_rndA,puncta_rndB,'K',5); %getting five other options
match_vector = zeros(si... |
7fc90fbc63ef1763c92c8ab389694c99078e811fda7b8165984f9900c6d748a5 | MATLAB | 2,120 | 60 | function rr = eq(aa, bb)
%eq - Test two CalibrationPixelSize objects for equality
%
% eq(OBJ1, OBJ2) tests scalar CalibrationPixelSize objects OBJ1 and OBJ2
% for equality, returning logical 1 (true) if the two objects are
% identical, or logical 0 (false) if they are not.
%
% See also CalibrationPixelSize, Cal... |
f24cde1377c5907a956136e814308b4370b7075cebadbd8ba6c494f4ee1d283e | MATLAB | 2,122 | 62 | function varargout = file_exists(val)
%file_exists - Check that the file exists
%
% file_exists('fn') checks that fn is a path to a file that exists. If
% it is, nothing else happens; if it is not, the function throws an
% exception from the calling function.
%
% ME = file_exists(...) returns the MException ob... |
21538dc2a9a257012ea0cecab647d70ab560b4c85c15369a3520cd52607714ba | MATLAB | 2,130 | 54 | %Helper function to be used to plot voxels onto coronal plane
function plotVoxelsOnMRIPlane(axis, intersectingVoxels, planeLabel, cursorPosition)
% Get the spm plotting object
global st
% bouding box for the MRI
boundingBox = st.bb;
sagitalBoundingBox = boundingBox(:, 1);
coronalBoundingB... |
3fa9fca546d9340e6720d8cbec101958e0bc2fd07dc6a227702946d3fcea4a83 | MATLAB | 2,130 | 103 | clear all
close all
gdfX='exampleRaceFile/raceEEG.gdf';
txtX='exampleRaceFile/raceLog.txt';
sampling = 512;
txtFile=txtX;
[signal,h]=sload(gdfX);
AA=readtable(txtFile);
nEvents=size(AA,1);
eventHeader=[];
for e=1:nEvents
string=char(table2array(AA(e,2)));
matchStart=string(1)=='s';
if(... |
b1602bf6b01d95c8a4fe8f802d60ac778c54850204e32c51ef8b66a4eb473301 | MATLAB | 2,131 | 78 | %sim_onepulse_arbPh.m
%Robin Simpson and Jamie Near, 2014.
%
% USAGE:
% out=sim_onepulse_arbPh(n,sw,Bfield,linewidth,sys,ph)
%
% DESCRIPTION:
% This function simulates a pulse-acquire experiment with an ideal
% (instantaneous) excitation pulse and an assumed lorentzian lineshape.
% The function calls the function 's... |
d2bfd765d50d7b26c0bc46e2bd06e87a6f4147829f5e70f500124f836211083f | MATLAB | 2,133 | 76 | %% consistency
%
% Calculate VAR model consistency
%
% <matlab:open('consistency.m') code>
%
%% Syntax
%
% cons = consistency(X,E)
%
%% Arguments
%
% See also <mvgchelp.html#4 Common variable names and data structures>.
%
% _input_
%
% X multi-trial time series data
% E re... |
9bccaf00db78030790dbbe8999e2c623abdd4d0c1cf718aa4121eefed846f7fe | MATLAB | 2,134 | 75 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [decorr_obj] = decorrelation(input,output,num_params)
%DECORRELATION Records normalised decorrelation of the spike trains
if nargin<3 || isempty(num_params)
num_params=struct;
end
if ~isfield(nu... |
a44b3761760e55a5d82dbdc7c170a9c048983ea2849c2ef5614ccfd1ec473abd | MATLAB | 2,137 | 65 | % op_dccorr.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [out,dcOffset]=op_dccorr(in,mode,var1);
%
% DESCRIPTION:
% Do a DC Correction on the data. This method is a frequency domain
% operation.
%
% INPUTS:
% in = input data in matlab structure format.
% mode = ppmrange('p') or Value('v'). In ppmrange mo... |
988cd14b35ae3a0fc992937c26be876d7d9094030481a227ed415ca2213a17f1 | MATLAB | 2,139 | 90 | % PL_TREE Topological path length.
% (trees package)
%
% PL = PL_tree (intree, options)
% ------------------------------
%
% Returns the topological (!!) path length PL to the root node in the tree.
% For metric path lengths use Pvec_tree.
%
% Input
% -----
% - intree ::integer: index of tree in trees or str... |
75806f8a713d04c2f3a86205c1d0ae19d71f46158b681ef14c2fe41f5ebb199b | MATLAB | 2,140 | 43 | function trialAveragedNormalizedROIs = trialAverageAndNormalizeArray(genotypeStimArray, targetTimes, stimStr)
[nPulses, pulseDurMilliSec, ...
ISIseconds, nTrials, ...
ledPowerLEDunits, stimDur, freqHz] = parseStimStrOptogenetics(stimStr);
% I should read the Mark_points.xml, but for now, I know the first stimulus
%... |
7c611533af58d437a24755445cbb6cdadd24e13cbbd4cf98caff58354ab9dae9 | MATLAB | 2,140 | 119 | %% plotLocationConsistencyCombined
clear all; close all; clc
%% Plot day-by-day spatial correlation
folds = findSubF('RBRLoc.mat',1,[],0);
% useIdx = [2 3];
% type = 'bad';
useIdx = [1 4 5 6];
type = 'good';
maxDay = 10;
RBRLocComb = cell(1,maxDay);
for ii = 1:length(useIdx)
load(folds{... |
88cd20ef0a27ef44d9a54203013e0c1ecf43883c1e3a5e850b4270a82dbbaf9e | MATLAB | 2,140 | 64 | function [lineOut, fillOut] = stdshade(amean, astd, alpha,acolor,F,smth)
% usage: stdshading(amatrix,alpha,acolor,F,smth)
% plot mean and sem/std coming from a matrix of data, at which each row is an
% observation. sem/std is shown as shading.
% - acolor defines the used color (default is red)
% - F assignes the ... |
ecb4590f306d65dd3823a05d9d82bbe7d62c52bef9f680835097046d7d040edb | MATLAB | 2,141 | 55 | function shuffle_synapses(rValue)
addpath('/lustre04/scratch/nbrake/code/simulation_code');
if(nargin<1)
comboID = 13;
end
comboID = 13;
mCombos = zeros(11*10/2,2);
count = 1;
for i = 1:11
for j = i+1:11
mCombos(count,:) = [i,j];
count = count+1;
end
end
folder = ['/lustre04/scratch/nbrake... |
7c969dcd7d4b451097489ee7942cc2ca71d3da6dc2dda4f8186df8cc2a3eadbb | MATLAB | 2,142 | 83 | load('figure_4_data.mat');
% plot median power spectra of the cortex and thalamus during waking,
% anesthesia, seizure, and 5-meo-dmt states
figure;
subplot(4,2,1);
inds=[find(freqs>=58.5&freqs<=61.5)' find(freqs>=118.5&freqs<=121.5)' find(freqs>=178.5&freqs<=181.5)' find(freqs>=238.5&freqs<=241.5)'];
freqs1=freqs;
ps... |
ed9b9241adc164acb9516c3d15bf43ec5db05a3dffd5a9dc9e52d9f892a565fa | MATLAB | 2,142 | 55 | %% power curve
clc;clear;close all;
%%
% This code plots power curve
% T-test, vary sample sizes
% effect size
Cohensd = 0.5;
% SD for normal distribution that governs the correlations of
% non-covariate-related edges
sigma0 = 1;
FWER_threshold = 0.05;
% Number of repetitions
M_rep = 100;
% Number of permu... |
410c01c53c6c8b53f2faad12b036573a9e1cfc99b305eb160b5eb8405a46762a | MATLAB | 2,147 | 63 | function varargout = not_empty(val, varargin)
%not_empty - Check that the value is not empty
%
% not_empty(val) checks that val is not empty. If it is, nothing else
% happens; if it is not, the function throws an exception from the
% calling function.
%
% not_empty(val, 'VarName') includes VarName in the excep... |
8add1dce3c36b843e5a88e48f79e5cd38530df1beba2c9a4f02867227db603b6 | MATLAB | 2,147 | 58 | function varargout = verify_license(feature, className, varargin)
%verify_license - Verify that a particular licence is available
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute i... |
575a8a8bc2cddec573bada0a6274ea9613781d637bc4909cc0745e38b705d7e5 | MATLAB | 2,149 | 66 | function cfg = validateConfig(cfg)
%VALIDATECONFIG Validate and normalize pipeline configuration.
required = ["phaseFile", "magnitudeFile"];
for name = required
if strlength(string(cfg.(name))) == 0
error('fmriPhase:config:MissingRequired', ...
'Configuration field "%s" is required.', name);
... |
8c30278ee9daaeee92f34fc3d86549dff7e21dbc2cd149f743bb63bae129988a | MATLAB | 2,152 | 54 | % Generate hybrid model input from EEG source activity
%
% USAGE:
% preprocess_external_input(output_fileid, source_activity, regionsMap)
%
% INPUTS:
% output_fileid - String that contains the filestem for the output textfile
% source_activity - [68 x 259184] matrix containing EEG source activity for
% ... |
9d3ddc1776a8d5f13bbd9684274e5e77c0f7539adba2c59ce422023ec7e15c77 | MATLAB | 2,153 | 50 | %Written for the first splintr barcode dataset from Oz
FOLDER_NAME = 'ExSeqAutoSlice';
FILEROOT_NAME = 'exseqauto';
for roundnum = 1:30
%Load all channels, normalize them, calculate the cross corr of
%channels 1-3 vs 4
chan1 = load3DTif(sprintf('/om/project/boyden/%s/input/%s_round%i_ch00fixed.tif',F... |
d68636e088dab371556b6fb3294700dfe1916506e53240cf6f7f0128ff6e89e0 | MATLAB | 2,154 | 68 | % Extract and downsample state variables from simulation results
%
% USAGE:
% statevars = extract_statevars(waveform_file)
%
% INPUTS:
% waveform_file - String that contains the filename of the ..txtwf
% waveform file output by the hybrid model C code
%
% OUTPUTS:
% statevars - struct that co... |
e9a133d492dd87fa71999728193088bf423f27b9259035562c7ae93234f7f449 | MATLAB | 2,154 | 66 | function [] = dispDistsPlots()
% Plot disparity probability distributions used for main figs in paper and controls
% Load in disparity histograms based on each KSD
load('./analysisFiles/disparityStats/dispHistStruct.mat');
% Define stats subsets
imgSet = {'sando','walking'};
region = {'Circ','V1','V2','MT'}... |
2960559841c4cdfed48daffce9f3df60211f71a993d03e9069336b09446db0b8 | MATLAB | 2,157 | 86 | % RINDEX_TREE Region-specific indexation of nodes in a tree.
% (trees package)
%
% rindex = rindex_tree (intree, options)
% --------------------------------------
%
% Returns the region specific index for each region individually increasing
% in order of appearance within that region.
%
% Input
% -----
% - intree :... |
06620f083bd539c4ded5b55d2de455c495d4ce1851af8304ecfebc26f58f3fc4 | MATLAB | 2,160 | 58 | %% power curve
clc;clear;close all;
%%
% This code plots power curve
% T-test, vary sample sizes
% effect size
Cohensf2 = 0.15;
% SD for normal distribution that governs the correlations of
% non-covariate-related edges
sigma0 = 1;
FWER_threshold = 0.05;
% Number of repetitions
M_rep = 100;
% Number of per... |
acd41610b364b4af0f7b02cd4ec70e3814e540f7c6a4cd5444080ad63dd10d52 | MATLAB | 2,161 | 58 | classdef Constants
% properties( Constant = true )
%
% end
%
methods (Static)
function d = getDir
output_dir = 'p1';
simulator_dir = 'p2';
sessionDate = 'p3';
d.analysisoption = 9;
d.sessionDate ... |
72e6bab22776c833b3e41f5d658cc7919268046540650c0a916bd6292d0e4383 | MATLAB | 2,162 | 67 | function varargout = plot_ROIs(self, objPI, hAxes, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, eithe... |
802aaac5a0911cf6929e64db678da68f1546ab614963e4f4c4681a7761aefa6c | MATLAB | 2,163 | 84 | % LOAD_STACK load stack file into a stack structure.
% (trees package)
%
% [stack name path] = load_stack (name, options)
% ----------------------------------------------
%
% loads a stack structure from a file.
%
% the stack structure as in "save_stack":
% stack has to be in the following form:
% stack.M ::cell-... |
90a726decdf119dabf6b3265ee69f9107576d17707ee8ed7fe8687603e684098 | MATLAB | 2,164 | 75 | % rf_blochSim.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [mv,sc]=rf_blochSim(RF,tp,fspan,f0,peakB1,ph,M0);
%
% DESCRIPTION:
% Perform a bloch simulation of an RF pulse. This code simply runs Martyn
% Klassen's excellent bloch equation simulator. For more information, see
% help file for bes.m. (~FID-A/rf... |
1bd0b5da9856358b32fefc81be8e7c96f0b9eae8d7a9d7fb1caa9c49200b019a | MATLAB | 2,166 | 75 | function [segregation, global_segregation]=systemsegregation(conn_mat, CA)
%conn_mat is the n x n input connectivity matrix. This matrix should only
%have positive connections
%CA is an n x 1 matrix containing modular assignments for each region n
%convert diagonals to 0
conn_mat(logical(eye(size(conn_mat))))=0;
%Onl... |
fb74188d19f2a86e95d9fe8f2a69e912b2da41128c348bbbaca01cf5dac05b11 | MATLAB | 2,166 | 60 | function model = addPenaltiesToModel(model, B, TM, TG, UCyto, UMito, dontPenalize, TMT)
% addPenaltiesToModel
%
% Adds EAMCA maintenance costs to the model
%
% Input:
%
% model The model to modify
%
% B Base cost - maintenance cost per protein unit without transportation or utilization penal... |
4bff6ba1c19648b400258160af62d7f476d3e65d40202b07d62e00d928236c5e | MATLAB | 2,167 | 67 | function X = taft_preprocess_load_fMRI(job)
% X = taft_preprocess_load_fMRI(job)
%
% Calls function for fitting HRF amplitude, reshapes into design matrix.
%
% INPUTS:
% job = structure with settings for creating TAfT object, specifically:
% .goodTrlIdxfMRI= numeric vector, indices of trials to include; to... |
96b06ee7b59a7939b0c08a8b89baf86a8000211e36dee730cbe9cba1cd243895 | MATLAB | 2,167 | 64 | function [hHG, plotName, idxStart] = check_plot_args(validPlotNames, ...
args, hgType)
%check_plot_args - Helper function to check and return plot arguments
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free s... |
b15ff7b85f6c930fab5a53a1c41b11a3cf7f6b2e1868c995a4d96bfafccde074 | MATLAB | 2,172 | 49 | function rawImg = from_files(varargin)
%from_files - Create a RawImgDummy object from a list of files
%
% OBJ = RawImgDummy.from_files() prompts for all required information and
% creates a RawImgDummy object.
%
% OBJ = RawImgDummy.from_files(FILENAME) creates an object from the
% specified filename(s). FILENA... |
d4b08e6e64fe055e94baa40b4ab5de71419a60e3a01885fe3f3a6a067e95f638 | MATLAB | 2,175 | 64 | % this code will read all the gaze files from the trials and covernt them
% to the image coordinate.
clear
close all force
warning on
imSize = [733, 977];
pix2deg = 34.910;
hWB = waitbar(0,'checking the trials ...');
%load tirals info
load('a0_0_bhv2trialStrct.mat');
I = arrayfun(@(x) isfield(x.analyze,mfilename),... |
6c1f7df299f1c879c8e4392aafabc0d7da340a45852a9f2d4aa551978ab5e5ba | MATLAB | 2,176 | 77 | function [loglik] = EEGfMRIPav_cbm_mod02(parameters,subj)
% Standard Q-learning model with delta learning rule and with Go bias.
% ----------------------------------------------------------------------- %
%% Retrieve parameters:
% 1) Feedback sensitivity:
nd_rho = parameters(1); % normally-distributed rho
rho ... |
1c559620f6c4b1d05021e313118a3aceb23307c49eed3de4c01d3e94069fd5d5 | MATLAB | 2,177 | 78 | %WORK IN PROGRESS
function out = op_CSISelectVoxels(in, x, y)
arguments
in (1,1) struct
x (1,2) double = [-1,-1]
y (1,2) double = [-1,-1]
end
global selected
selected = [];
if(x(1) < 0 && y(1) < 0)
fig = sim_plotCSI(in);
ax = fig.Children(1);
set... |
59880da44827755723e01c34972e1318ac2745fbc1a0c5c625373539f5997b21 | MATLAB | 2,177 | 85 | % RATIO_TREE Ratio between parent and daughter segments in a tree.
% (trees package)
%
% ratio = ratio_tree (intree, v, options)
% ---------------------------------------
%
% Returns ratio values between daughter nodes and parent nodes for any
% values given in vector v. Typically this is applied on diameter, but:
%... |
1f012cdc707cdf9c96b40e392dc0c4fb742937d5c2b60f058a7da9734fc634c2 | MATLAB | 2,179 | 76 | % SMOOTHBRANCH Smoothen points along one path.
% (scheme package)
%
% [Xs, Ys, Zs] = smoothbranch (X, Y, Z, p, n)
% -------------------------------------------
%
% smoothes a branch given by consecutive (!) 3D coordinates. This changes
% (shortens) the total length of the branch significantly.
%
% Input
% -----
% - X... |
72e6e9a7d9dd9af6ce325753decdc2157fa127bcf4bd53e41314710092125ec6 | MATLAB | 2,181 | 83 | function y = nanvar(x,flag,dim)
% FORMAT: Y = NANVAR(X,FLAG,DIM)
%
% Variance ignoring NaNs
%
% This function enhances the functionality of NANVAR as distributed in
% the MATLAB Statistics Toolbox and is meant as a replacement (hence the
% identical name).
%
% NANVAR(X) calculates the variance along t... |
d076c4fd2909176a23813b570ec069c2d383dcf5919e8c4657315c6dad9373e0 | MATLAB | 2,182 | 57 | function makeText(display,stimulus)
% makeText(display,stimulus)
%
% Purpose
% Generate text which can subsequently be flipped onto the screen.
%
% Input
% display - Generated with loadDisplayParams and openScreen.
% stimulus - Structure containing text parameters.
% .text - String to be rendered.
% .xP... |
006510abe0b48626e74f3b190d54a80233df3e20cb436fabc8b66e0af5e4b23a | MATLAB | 2,186 | 85 | function [corrStats] = corrEffectSize(data1,data2,testName,nUnits)
% Performs two-tailed pearson linear correlation. Outputs all statistics in
% a cell array. Can be used to manually generate correlation information
% for compliance with journal manuscript requirements. If only one data
% matrix is input, a correla... |
ab312c6c031d1f422331b5501bd6b98c7adbdaf4f2de22ea4dace0d7317079ad | MATLAB | 2,186 | 52 | function install_bfmatlab(varargin)
%install_bfmatlab - Install the files required for Bio-Formats
%
% install_bfmatlab() installs the files required for Bio-Formats from the
% Open Microscopy Environment website to the subdirectory bfmatlab within
% the CHIPS root directory (as returned by utils.CHIPS_rootdir). ... |
3bc9c95e578acf88e990bce4211c60555faae4439938fe8c61341224e204eca9 | MATLAB | 2,188 | 57 | function [windows, time, yPos] = split_into_windows(self, windowTime, ...
nOverlap)
%split_into_windows - Split the raw image data into windows
%
% [WINDOWS, TT, YY] = split_into_windows(OBJ, T_WINDOW, N_OVERLAP) splits
% the raw image data into a matrix WINDOWS, and also returns the time
% value (TT) and ve... |
8947072f9fc3656d57d075f127d694ea4b0671e74805c085cd8fa665084e74d8 | MATLAB | 2,195 | 58 | %RunElectodesClassificationMatlabFunc
clear all
matlabImpute = true;
imputeIters=20;
%NumTreesVec = [10,20,40,80];
NumTreesVec = [80];
substractMouseMean = true;
%LeaveOut = 'Stimuli';
%LeaveOutVec = {'Stimuli','Session','mouse'};
LeaveOutVec = {'mouse'};
%ElectodesClassificationMatlabFunc(unifyContextClasses... |
0d5add75d5af17282db1f723bd7ebb65c527e24d83d51c080c76a77e7f5d13d2 | MATLAB | 2,197 | 46 | %% READ ME:
%
% Written by Zachary Sanger, M.S.
% University of Minnesota
% Biomedical Engineering Department
% May 16th, 2023.
% IF YOU FEEL THERE ARE ERRORS, please reach out at sange019@umn.edu!
% please cite if you use the code
%
% For informal use only, please double check your code for validity and proper imp... |
226127df006e29f2fe30c1618a88ec65947b2f6860554e4533f4b5721068d83a | MATLAB | 2,198 | 58 | %% power curve
clc;clear;close all;
%%
% This code plots power curve
% T-test, vary sample sizes
% effect size
Cohensf2 = 0.15;
% SD for normal distribution that governs the correlations of
% non-covariate-related edges
sigma0 = 1;
FWER_threshold = 0.05;
% Number of repetitions
M_rep = 100;
% Number of per... |
b7a313d8f37c65b057f6e8d19480df030304b59af496179559397950699abb60 | MATLAB | 2,199 | 88 | % PVEC_TREE Cumulative summation along paths of a tree.
% (trees package)
%
% Pvec = Pvec_tree (intree, v, options)
% -------------------------------------
%
% Cumulative vector, calculates the total path to the root cumulating
% elements of v (addition) of each node. This is a META-FUNCTION and can
% lead to variou... |
3a7b4b7c67fabe58e47fdfe4f8ac0f6e1d17d8631d1e2e8ffe0485acf0d1dc4d | MATLAB | 2,201 | 58 | function h = t2n_plotTrees(tree,targetfolder,col,ostruct)
% This function plots each tree in a nice way and saves them as eps files,
% eg for using in Adobe Illustrator.
%
% INPUTS
% tree TREES toolbox tree cell array
% targetfolder target folder for output files
% col (optional) cell array with rg... |
69fbd7ddc5a788db08ac7622e7581297f21077deb0242eb5515cdd12fd909325 | MATLAB | 2,201 | 67 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [binned_spikes]=bin_outputs(output,output_code,binsize_ms,max_time,wordsize)
n_trial=size(output,1);
n_rep=size(output,2);
if nargin<4 || isempty(max_time)
max_time=0;
for ward=1:n_trial
... |
efa2aea978bfdd880219c11a0fd5b8c8d2801d31dc52507b8936d0a84c704687 | MATLAB | 2,205 | 57 | function [DataMatrix, Labels,MouseIDs,Days,sessionNames, stdMatrix] = AverageSessionData(DataMatrixSrc, LabelsSrc ,MouseIDsSrc,DaysSrc,sessionNamesSrc)
sessionNum = zeros(1,length(sessionNamesSrc));
SessionNameWithoutBout = cell(1,length(sessionNamesSrc));
for k=1:length(sessionNamesSrc)
curName = sessionName... |
f54b5b5849260f496f78859667ae6abc93afa8d4a574f3b877c20eb05666d8fe | MATLAB | 2,205 | 98 | function [fn, savename] = st_plot_optHRF(hrfTable,sumTable)
% hrfTable = cleanHRFtable(hrfTable);
% hrfTable= tableRemoveHRFDuplicateCoords(hrfTable);
% sumTable= tableSumHRF(hrfTable);
%%
fn = figure('position',[0 0 1500 500]);
savename = ['hrfs'];
% figure panel 1
params=[];
roiList = {'V1','V2','V3','hV4','VO','... |
1b3dff1f145e00c936f387eb51727d2cacaf28ff5029ea9c149b28dc9d30350b | MATLAB | 2,209 | 83 | function [out] = EEGfMRIPav_cbm_mod01_osap(parameters, subj)
% Standard Q-learning model with delta learning rule.
% ----------------------------------------------------------------------- %
%% Retrieve parameters:
% 1) Feedback sensitivity:
nd_rho = parameters(1); % normally-distributed rho
rho = exp(n... |
6568b6574e05e65cedd66989b05b2bfdf47ea0ce457d5c950662627e26833623 | MATLAB | 2,209 | 52 | function [W_DSD_greedy, Clist, CID] = greedy_multiple_CID(Wp, func, threshold_DSD)
% GREEDY_MULTIPLE_CID performs a greedy clustering algorithm on a weighted graph.
% This function applies a greedy peeling algorithm to identify clusters in the graph.
% The algorithm iteratively finds clusters until the average value... |
74204c76a1938ddf8f9dd8c17c4eb9472b2904d8c100e232bd188bdd85a32dc2 | MATLAB | 2,212 | 91 |
clear
close all force
warning on
imSize = [733, 977];
load('a0_0_bhv2trialStrct.mat');
NIm = {[1:62]};
%{
I = NIm{1} == [...
1
3
15
16
21
22
32
33
34
43
46
54
58
61
62];
NIm{1}(any(I)) = [];
%}
NIm{1} = NIm{1}';
tic
%nMuscimol = numel(dataExp.sMuscimol);
%UMuscimol = [0,12,9,4,1];
UMuscimol = [0, 12,9 ... |
193cd88efc00979c37e514166c6121ed1452ad544ff96ec9635b9c68ee1dac79 | MATLAB | 2,213 | 42 | function [TwoAnimalsInteractionTimeInSec, DistanceBetweenTwoAnimalsPixelPerSec]=...
Analyze_Free_Video_Results_23012020(filenameBehavioralVideoData,FramesTimesInSec,AssumedFrameRateVideoCam1)
%TRACKMICEPOPULATIONSUMMARY Summary of this function goes here
% The aim of this function is to extract the results of a v... |
80e5d63419f812f28bf1eead4fd0b28b77a4660e0944877430ea4e8341884699 | MATLAB | 2,213 | 64 | function details = checkForNewVersion
% Check whether there is a GitHub release with a new version of the software
%
% details = zapit.updater.checkForNewVersion()
%
% Purpose
% Use GitHub's releases and the local reported version number to decide
% whether there is a new version up on GitHu... |
180709e9b51a2cc5eb969028dcd6a345f67c3debcab43bbb2f67e73dd6ba5d92 | MATLAB | 2,214 | 65 | function betas = taft_preprocess_fit_HRF_trial(job, data)
% betas = taft_preprocess_fit_HRF_trial(job, data)
%
% Take upsampled data epoched into trials, fit separate HRF per trial.
%
% INPUTS:
% job = structure with settings for creating TAfT object, specifically:
% .add_intercept= whether to add intercept... |
efc577e40585bdb33644b7e4c7f9233e59c8e55ea27353429cefd264f1333736 | MATLAB | 2,214 | 51 | %Written for the first splintr barcode dataset from Oz
FOLDER_NAME = 'ExSeqAutoSlice';
FILEROOT_NAME = 'exseqauto';
for roundnum = 1:30
%Load three of the channels, ignoring ch02
chan1 = load3DTif(sprintf('/om/project/boyden/%s/input/%s_round%i_ch00.tif',FOLDER_NAME,FILEROOT_NAME,roundnum));
chan2 = load3D... |
d4c0234c354f603877a57babe7c6d851567229f62c0a975434f23b9bab4edfc2 | MATLAB | 2,217 | 81 | rand('seed',0)
randn('seed',0)
N_1=500;
N_2=500;
N_3=0;
GeneralNoise_N=50;
N_SubClusters1=10;
N_SubClusters2=10;
x_c1=1-0.2;
y_c1=1;
x_c2=1+0.2;
y_c2=2;
x_c3=x_c1+0.8;
y_c3=y_c2+1;
R1=1;
R2=1;
R_noise=0.05;
SD_x_3=0.1;
SD_y_3=0.1;
Y_factor=1; %straching(/squeezing) y vs x
GeneralNoise_xRange=[0 2];
GeneralNoise... |
4568ee2cb360f8bd5596dded80ddeaabe4bae3a2dfccd1e376575542dfd27571 | MATLAB | 2,218 | 59 | function channelToUse = choose_channel(chsAvail, chsReqNames, procImgType)
%choose_channel - Helper function for choosing channels
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute ... |
5f721c2832598820b9dd71692a3556266a3e12b257e3e5ea0291ed14e7683ad0 | MATLAB | 2,218 | 93 |
clear all
close all
currentdiectoryLocation=pwd;
addpath(strcat(currentdiectoryLocation,'/functions/'))
[decoder.preprocessing.bandPassFilter.b,decoder.preprocessing.bandPassFilter.a]=butter(2,[8 30]/(512/2));
dataLocation = 'expertMIData';
allRunsInfo = dir(fullfile(dataLocation, '*.gdf'));
nRuns=size(all... |
cd0441b9a9f4a68989f861986ac513d33aeea7c31f6485bbb9d484e962023e8c | MATLAB | 2,219 | 52 | function [X_train,Y_train,X_test,Y_test,p,nmax]=problem(xx)
% Input and preparation of the training and testing data for the NN model
warning off
if xx==1
filename='Loan-Approval-Prediction.csv'; % Example 1
data=readtable(filename,'ReadVariableNames',true,'ReadRowNames' ,false,'TreatAsEmpty' ,'-');
... |
a9c2093506dfd6e269b7c5a850e80ce08b9d4e235e39d42ab8d723b419c71dce | MATLAB | 2,220 | 63 |
clear all
averageAllBoutsFromSession = true;
substractMouseMean = true;
useStdMatrix = false;
maxUnknownsEquationsRatio = 0.5;
rng(0)
load('AllBouts.mat');
for k=1:length(sessionNames)
sessionNames{k} = [sessionNames{k},'_MouseID',num2str(MouseIDs(k))];
end
if averageAllBoutsFromSession
[Da... |
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