sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4b639324d0d4b0fa00129119603e4bc08d39e7738bf2e684b29b4f6c3238d386 | MATLAB | 2,590 | 81 | %% you need to change most of the paths in this block
function rez = my_prog_master(path_output, is_new_layout)
% Master script of the KiloSort2 pipeline, adapted to process the RIFF NA.
%
% Created by AlexKaz 02.2020
ops = create_my_prog_ops();
ops.fproc = fullfile(path_output, 'temp_wh.... |
6dc1812bcb797503d1af7f9922ddb144b33ddde79ed80028bdcce055e7461384 | MATLAB | 2,594 | 91 | % checkKiloSortOutputs
% Made by BMC - 9/28/2020
% Take Kilosort, individual trial align, plot rasters
% Take Kilosort, all visual event median and mean, plot SDFs
%Kilosort outputs are in .rez file.
clear
close all
PostSetup('brock')
global SORTDIR CODEDIR STIMDIR
cd(STIMDIR)
load('PhyPref.mat') %Matlab versio... |
126d17c70915645c31faa623b738e8e17fab2dee096125192fc3c85b38ed72d7 | MATLAB | 2,602 | 90 |
clc
clear
close all
sample_neuron = 68;
load xx_108_4_single_e2o_perf
exe2obs_cell = cellfun(@mean, test,'UniformOutput',false);
exe2obs = cell2mat(exe2obs_cell);
exe2obs = exe2obs-100/3;
load xx_108_4_single_o2o_perf
obs2obs_cell = cellfun(@mean, verif,'UniformOutput',false);
obs2obs = cell2mat(obs2obs_cell);
obs2... |
214b4038157dc996812f08ad5e27f7d51228a0a8097aa789ce230e8e8cdc63dc | MATLAB | 2,602 | 100 | function visIDX_EffectofTuning(IDX,dataType)
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).tm;
ThisCodeDidNotProduceExpectedResults_CheckForBug
uctLength = length(IDX.allV1);
% B. pull out all laminar matrices 3x(6,450,el#)
%preallocate
SDF = nan(size(IDX.allV... |
a517c6549336b1dacc533def5da6c5d54b761c0c21d81624ded12149b68a4fa1 | MATLAB | 2,604 | 42 | %-----------------------------------------------------------------------
% Job saved on 19-Feb-2020 14:40:45 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
function matlabbatch=spm_anat_segmentation(Dir_ana... |
dc5601bfca4d2be0c909974667e58791bf1e6e70ee367186ac3c8668077b2363 | MATLAB | 2,605 | 70 | function [brightFactor, frameNo, endFrame] = playTif(inputFile)
% PLAYTIF plays given tiff + getting frames brighter.
% Params:
% inputFile - name of the .tif file.
% from - frame to start the TIFF from.
%
% Run example:
% playTif('animation.dual_test3.tif')
%
% ... |
d5bc4afe4f348dcbc4470ec5e062f23ba8b0683b7621a270d20612c357c794e5 | MATLAB | 2,610 | 76 | function [Mean, V, phase, amp, A, B, C] = Compute_mean_variance(P, D, eta, is_stack, M, s, phase, w_mean, w_max)
%{
Compute the theoretical mean and variance curve, also the corresponding
phase. For special case, compute the constant term of the variance A.
Parameters:
P, D: constant of learning
eta: number of ... |
da94efd392a1604279f87835376947625e26dff805a0d2807a693d71f5d683cd | MATLAB | 2,610 | 73 | function setupSystem(saveFileDir)
%SETUPSYSTEM sets up the system for use of PsychDetect.
% Arguments:
% saveFileDir - full path to base directory to which experimental data
% will be saved. [default: 'HOME/experiment_data']
%
% setupSystem will create a directory 'experiment_config' within your
% home di... |
fc9ed8cf9fd5623327f227320f0c644ff005d1a5ba5218fc70e971cb0964fd96 | MATLAB | 2,610 | 91 | %%
% Simulation results for the spatial model for networks with and without
% astrocyte ensheathment of exc synapses
%%
% Default network with no spatial correlations
load('./CompressedData/Spatial/default_net_ex1'); load('./CompressedData/Spatial/astro_net_ex1');
% Default network with spatial correlations
load('... |
7b21a252438842fc0226669e6207de64ed1e5389778342c4aea930a6e03ae84d | MATLAB | 2,611 | 98 | %%
% Make a raster plot
% 1000 neurons are plotted, split between the population
%%
function plot_raster(times, tinds, Ntot, Npop, Ncells, pinds, plot_num )
% color_scheme = [0.8500 0.3250 0.0980;
% 0 0.4470 0.7410;
% 0.4660 0.6740 0.1880;
% 0.3 0.3 0.3];
% color_scheme = [81,128,68;
% 255,0,0;
% ... |
bd1639aff414ed2a83cb9c2b3e71e2148f79855e9b569a26c69a3f17a0a761cd | MATLAB | 2,612 | 86 | % Main script for the RIFF pipeline.
% This script processes data recorded from the RIFF
% For instructions, see https://github.com/jniediek/RIFF_publication/wiki
% We provide two sample recording sessions to illustrate the usage of this
% code
% 1. A ten minute session without neural recordings
% https://figshar... |
2693f8dd06b104095913ad77d1fb4fd99345bc3100964d825c88afc03a18df4a | MATLAB | 2,618 | 85 | function gramm_2x2_subline_NSNDEvariation(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);... |
978d4c412d42fc7576b2135464c5cadd8e9f398a70ad167c9d8b11484cebe9b0 | MATLAB | 2,624 | 90 | function check_mdp_timing(mdp_table, stats, fig)
% JN 2020-04-28
figure(fig)
if ismember('strig', mdp_table.Properties.VariableNames)
mode = 'strig';
else
mode = 'ttrig';
end
switch mode
case 'ttrig'
% specific to this method: find points where the ttrig column increased
ts_idx = f... |
b8a0a71a6f9cc8aa2762e8a2b0fef8c81634a9617a6755db3c5dbd9ad6e110dc | MATLAB | 2,624 | 83 | %%
% Creates the connection matrix
% Function Inputs
% Ne: number of excitatory, Ni: number of inhibitory
% Kab: # of connections between neurons of type a and b
%
% Function Outputs
% Vectors of the target/firing neurons pairs and the number of connection
% Connections are chosen with replacement, so neurons can conne... |
0a2f4bca703bc8ff3c1029596b882ed8d1e739faf575a4a2bfa91f611eefbee0 | MATLAB | 2,631 | 89 | function [data_subSUB,data_subORG,varnrm] = tdrSubspaceProjection(data_fulORG,subpars,plotflag)
% tdrSubspaceProjection Project population response into subspace
%
% Inputs:
% data_fulORG: population response in orignal space (original basis)
% subpars.subSUB_fulORG: projection matrix from original space (original
% ... |
54d76ac3b9e5fb0e640ecec6c0b07e13c431251123f919d19027ba5ed87cd324 | MATLAB | 2,632 | 56 | %% Reshape data for prior direction
clear; clc;
for m = 1:2
if m == 1
load('Data_A_trial.mat');
else
load('Data_B_trial.mat');
end
dataT = struct('unit',[],'time',[]);
%unit
dataT.unit = struct('response',[],'task_variable',[],'dimension',[]);
for i = 1:size(c1,2)
... |
3c002d051a1b6742b3ee152c9ebd24af16579fd0b3ba645a39bb4af59b6b9824 | MATLAB | 2,640 | 123 | function [MOV_DATA,FRAME_IDX]=fb_retrieve_mov(FILE,varargin)
%fb_retrieve_mov retrieves the movie data for a split mat file (the mat
%files in the 'mat' directory created by fb_data_split)
%
% [MOV_DATA,FRAME_IDX]=fb_retrieve_mov(FILE,varargin)
%
% FILE
% specify the filename to process, if left empty the user is prese... |
b74309c851450d610471c3e4a01bb66649278b594c9a62b56fd49a0226c668dd | MATLAB | 2,653 | 85 | function tdr()
% The TDR ('Targeted Dimensionality Reduction') toolbox implements the
% dimensionality reduction methods described in the paper:
%
% 'Context-dependent computation by recurrrent dynamics in prefrontal cortex'
% by Mante, Sussillo, Shenoy, and Newsome, Nature, 2013.
%
% The neurophysiology and behavior... |
0a649fa1d8d3fd5a6e1329b8cef7d51e1260146bdc94bb722140c44ada83b635 | MATLAB | 2,658 | 60 | function ops = create_my_prog_ops(ops)
%
% ====== CHECK OUT THIS PAGE FOR PARAMETER SPECS:
% https://github.com/cortex-lab/KiloSort/wiki/Config-Variables#Nfilt
%
if nargin == 0
ops = struct();
end
% ops.chanMap = 'D:\GitHub\KiloSort2\configFiles\neuropixPhase3A_kilosortChanMap.mat';
... |
613ab9d6f4992f247abaa909774f82146f155f7c76627807c9e2aeb8a7717e62 | MATLAB | 2,658 | 95 | function Img = func_DrawLine(Img, X0, Y0, X1, Y1, nG)
% Connect two pixels in an image with the desired graylevel
%
% Command line
% ------------
% result = func_DrawLine(Img, X1, Y1, X2, Y2)
% input: Img : the original image.
% (X1, Y1), (X2, Y2) : points to connect.
% nG : the gray leve... |
a5c67dcf1012c338e7824f02dcf4cca03307350eea65046a0c33a2d40e969b10 | MATLAB | 2,661 | 112 | %% distance in subspace
clear; clc;
%load data
load('subspace_position_A.mat');
a = sdata;
load('subspace_position_B.mat');
b = sdata;
%
ah_dis = []; al_dis = []; bh_dis = []; bl_dis = [];
ah_wx = []; ah_nx = []; al_wx = []; al_nx = [];
bh_wx = []; bh_nx = []; bl_wx = []; bl_nx = [];
for n = 1:27 %time=101:20:621(w... |
9e08dbb085b683f68e3ba8fccea976e27255d22c4dc642a430ebc191e2f4ec3e | MATLAB | 2,671 | 56 | %% Reshape data for all directions (prior direction, two outer directions)
clear; clc;
for m = 1:2
if m == 1
load('Data_A_trial.mat');
else
load('Data_B_trial.mat');
end
dataT = struct('unit',[],'time',[]);
%unit
dataT.unit = struct('response',[],'task_variable',[],'dimension'... |
7cae97bafa8e6aede39b9cbbf42dbd2146c544df828bee07939b4b98284578a1 | MATLAB | 2,672 | 94 | function data_nrml = tdrNormalize(data,nrmlpars)
% tdrNormalize Normalize population responses
%
% Computes R* = (R - m)/(s + c)
%
% R* are the normalized responses
% R are the raw responses
% m is the mean across trials/conditions and time
% s is the standart deviation across trials/conditions and time
% c is a ... |
0a9fd5ca67d6ab1c722a8eb54d7cda6b5922c4b996ee5a875ee534de502ab3af | MATLAB | 2,674 | 64 | function [valid_flag,err,is_formula]=check_if_legal(comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given val as a Ramp_comp-object property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(COMP,PROP,VAL,DEF_ARR,
% VAR_ARR) checks that VAL is a legal value for the Ramp_comp-object property-PR... |
e319a6f49b568a07b839c0731d245f31d4154079cb06b4facdeecfbf4797e3d6 | MATLAB | 2,674 | 90 | function [countsNoNoise] = gui_FFTfilter_old(counts, gauss_blur_radius, spectral_radius, scaling_factor)
% Scale the image
im = counts * scaling_factor;
% Mean of all values
mean_value = mean(im(:));
% Center the distribution
im = im - mean_value;
% Add custom blur
if gau... |
ed84d4f7c919954216c9924437dcd09e2bc9827f2559d7389663d6c035e3ae52 | MATLAB | 2,674 | 80 | function h = dmaxflat(N,d)
% returns 2-D diamond maxflat filters of order 'N'
% the filters are nonseparable and 'd' is the (0,0) coefficient, being 1 or 0 depending on use
% by Arthur L. da Cunha, University of Illinois Urbana-Champaign
% Aug 2004
%
% Part of the Nonsubsampled Contourlet Toolbox
% (http://www.mathwor... |
d098536cbb5838ab3673e929834ecc7440c4fba5bfb32e59dfe48bde4b3b8f57 | MATLAB | 2,677 | 96 | function [ filtered ] = frst2d( image, radii, alpha, stdFactor, mode )
%FRST2D Applies Fast radial symmetry transform to image
% Check paper Loy, G., & Zelinsky, A. (2002). A fast radial symmetry transform for detecting points of interest. Computer Vision?ECCV 2002.
% Three different modes are available: 'bright', ... |
ec2c4d31fee9e503f40b3e358c93eb4d4ede8ca808dbc3b068d66efd42b7a402 | MATLAB | 2,680 | 67 | %Author: Tatjana Schmitt 2019-2022
function [boundaries, complete_boundaries_map] = borders_map(edges_turning_points_maps)
% smoothes coordinates and combines to one map
number_of_ones = zeros(1, size(edges_turning_points_maps,2));
for ii = 1:size(edges_turning_points_maps,2)
number_of_ones(1,ii) = sum(edges... |
2afac74d3e30120ba66319524495083c650c77019a5c40a31d5fa19d6e831ee9 | MATLAB | 2,688 | 90 | function gramm_2x2_subline(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);
clear DataFor... |
48e3aeea7de8c233b03e3871ddfd6051b358134bf3ff8555233aeadcd404a770 | MATLAB | 2,688 | 68 | % [kcMap,A0Map] = getLocalDcorr(im,tileSize,tileOverlap,r,Ng,figID)
% ---------------------------------------
%
% Estimate the image local cut-off frequency based on decorrelation analysis
%
% Inputs:
% im 2D image to be analyzed
% tileSize Size of a tile in pixels
% tileOverlap Spatial overlap between tw... |
cdc3408c31510e526ea7735c273cd71f4add322a8e697769dd6d759f7001765d | MATLAB | 2,688 | 83 | classdef NewTrialState < LogbookState
%NEWTRIALSTATE happens when an AudioObject has been played.
% Author: Lasse Osterhagen
properties (SetAccess = private)
trials = cell.empty;
shamTrials = cell.empty;
ignoredTrials = cell.empty;
ignoredShamTrials = cell.empty;
audioObjects = cell.empty
... |
c0f854bb1965884253b1ce4c94fcb3242d41bb73b25e2edc403a19af3d9e6a1e | MATLAB | 2,696 | 81 | function [Mean, V, phase, amp, A, B, C] = Compute_mean_variance(P, D, eta, is_stack, M, s, phase, w_mean, w_max)
%{
Compute the theoretical mean and variance curve, also the corresponding
phase. For special case, compute the constant term of the variance A.
Parameters:
P, D: constant of learning
eta: number of ... |
1e706a14e862b7bf03e7163dc8ad6cd90a42d2e740c43d5ec55aa9a08b7b98f7 | MATLAB | 2,697 | 74 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <normTimeseres: calculates %change from baseline signal >
%
% 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 ... |
b02140c8f15d080783cc6bd6ba545a2a534aaa94277dbe36e3efbf156094d6b3 | MATLAB | 2,717 | 73 | function plot_r21(rtData,diffData)
% rtData: 5 subjects X S1/DLPFC X speed/accuracy
% diffData: 5 subjects X S1/DLPFC X speed/accuracy
number_subjects = size(rtData,1);
figure
%% 1: Mean RTs
subplot(2,2,1)
bar(1, mean(rtData(:,2,2)), 'b', 'BarWidth', 1);
hold
bar(4, mean(rtData(:,2,1)), 'r', 'BarWidth', 1);
bar(2, me... |
bf88fe7fc2b49b0a5ee1b4b0ff7bafdd4a8984161196f0fc067e2bd3e6562716 | MATLAB | 2,717 | 83 | function out = extractCharacterStream(nevStruct, triggerBit)
% extractCharacterStream(nevStruct, [triggerBit = 1] extracts characters
% from the digital input data of a Blackrock NEV-file.
% The output is a 2-by-N cell matrix with the first row representing the
% sample number of the stream starts and the second row th... |
6cad6f171592f725a2a9efba25e7380554b28369b5b1cec8466b3d9b0df0fe93 | MATLAB | 2,718 | 87 | function gramm_adaptation_RESP(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);
clear Dat... |
50a8c05105b8650062d008b6ff3a28c9fe04cbe868a98b4d71e7771a2dc2ddd5 | MATLAB | 2,719 | 89 | classdef ImageDescription < handle
properties
descstr
dict;
keys;
end
methods
function obj = ImageDescription(varargin)
if numel(varargin)==1
obj.descstr = varargin{1};
elseif numel(varargin)==0
obj.keys = {
... |
f60d1da8b068df2c20da844ee24345ed5d12cf672cac5ef648439e858abf649b | MATLAB | 2,720 | 79 | %% This scripts loads MEG connectivity and power values for each subject and resamples them for functional resting-state networks
% (Yeo et al., 2011; https://doi.org/10.1152/jn.00338.2011)
%
% Written by Christina Stier, 2022
% load surface description for remapping from suma vertex-resolution to yeo-networks
load('... |
2c5734daa9afb96fdb055899bbf5cbeedbdb534903fefeb4225df26f56a2516e | MATLAB | 2,728 | 79 | function sampled_points=generate_signal(handles,trial_index)
% GENERATE_SIGNAL generates the sample points of the Signal.
% SAMP_RATE=GENERATE_SIGNAL(SIG,SAMP_RATE,PARAMS) generates the sample
% points of the given Signal. The number of points is determined by the
% given samp_rate.
% params is a collumn vector that h... |
154e92210f448434e60a8ee5ea557afac13d88f75086d0d326219ef59a42be03 | MATLAB | 2,731 | 69 | function [valid_flag,err,is_formula]=check_if_legal(comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given val as a Freq_comp-object property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(COMP,PROP,VAL,DEF_ARR,
% VAR_ARR) checks that VAL is a legal value for the Freq_comp-object property-PR... |
933a9d5c022b8d59188efc51fcd8db04c721cfb69e071875354ef7214bc007e3 | MATLAB | 2,731 | 86 | function values=get_values(coord,comp,crid)
% GET_VALUES returns the table of values of the component.
% VALUES=GET_VALUES(COORD,COMP,CRID) returns the table of
% values of the given component.
% CRID is the coordination index that define the order that the
% values of this component will be taken relative to the oth... |
bfaac102887e5b9872bd5623f7b9b8420236eb719e4be5f7ecd8cab8ac1d3896 | MATLAB | 2,731 | 66 | function [valid_flag,err,is_formula]=check_if_legal(comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given val as a STime_comp-object property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(COMP,PROP,VAL,DEF_ARR,
% VAR_ARR) checks that VAL is a legal value for the STime_comp-object property-... |
032a254ddcaad50cc8ca332202458aab66754216549a00267311906b3647639c | MATLAB | 2,742 | 125 |
function FS_AV_Parse(DIR,varargin)
% FS_AV_Parse
% Parse Data from FreedomScopes
% Created: 2015/08/02
% By: WALIII
% Updated: 2015/04/18
% By: WALIII
% FS_AV_parse will do several things:
%
% 1. Seperate Audio and Video, and place them into .mat files in a .mat
% directory
% 2. Make spectrogram .gi... |
ef01e3d8052e8574f334aaee2569e91ca6695b04b44fdf67067073015c5ea509 | MATLAB | 2,752 | 97 | function res=check_params(varargin)
% res=CHECK_PARAMS(PARAM1,VAL1...) checks the validity for a Sweep object.
% Checks that PARAM1 field can hold the given VAL1 value and the same for
% PARAM2,VAL2 and so on.
% If all params are legal - returns 1. Otherwise returns 0.
global SWEEP_MAX_TRIALS;
global SWEEP_MODE_NAME... |
417c4793ff24d4ef041f7866c937f9dd02e1ebcd0f807bbcf6f0d9f954ac2c21 | MATLAB | 2,754 | 66 | function [valid_flag,err,is_formula]=check_if_legal(comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given val as a STime_comp-object property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(COMP,PROP,VAL,DEF_ARR,
% VAR_ARR) checks that VAL is a legal value for the STime_comp-object property-... |
588d97bde6b0a6a285675e4f1a23d01a2305a5bbbcda3b52da54d4d1f5f0257d | MATLAB | 2,757 | 127 | function [mask,mu,v,p]=EMSeg(ima,k)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Expectation Maximization image segmentation
%
% Input:
% ima: grey color image
% k: Number of classes
% Output:
% mask: clasification image mask
% mu: vector of class... |
342bff3c1a89eb847a8b89fbff70bb97b2631e521b57d89297a3cc8783776b2f | MATLAB | 2,776 | 93 | function gramm_dCOS_RESP(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);
clear DataForVi... |
c756faaf792e0cf051a3626a5fa5efa1b324ac9ebcf0be352d52b37c7487e926 | MATLAB | 2,776 | 90 | function plotAdj(data,sortIndex,categoryColorOpts,plotColor,suppresstext)
newROICount = [];
if length(categoryColorOpts)==3 && isvector(categoryColorOpts)
colorVals = [139,0,0;...
0,128,0;...
0,0,255]/255;
newROICount = categoryColorOpts;
elseif isvector(categoryColorOpts)
colorV... |
4c76e444583e15349aa130af11f7f5a49afcba726488b6cd09608bdf491f73da | MATLAB | 2,780 | 70 | function B_fitting(datswitch)
load('A_dataload.mat','NE','NM')
switch datswitch % choose between near miss and narrow escape data
case 1
dat = NE;
case 2
dat = NM;
end
name = dat.outcomename;
EEGtime = dat.eegtime;
EEGdat = dat.eegcurve;
beh... |
bc99530244385ef6df68bc2e39016d9229f9bbb6b9c9533c6ad6216515d17efb | MATLAB | 2,785 | 66 | function [valid_flag,err,is_formula]=check_if_legal(comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given val as a Trial_dur_comp-object property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(COMP,PROP,VAL,DEF_ARR,
% VAR_ARR) checks that VAL is a legal value for the Trial_dur_comp-object ... |
2c47e2d4ec60b57e34f3e9df0d12ffa6dc4e4b072d289eb067ada44ccfefdc04 | MATLAB | 2,794 | 61 | function [Z_MIP, phi_MIP, Zs, phis] = MIP_search_probs( probs, options)
%-----------------------------------------------------------------------
% FUNCTION: MIP_search_probs.m
% PURPOSE: Find the Minimum Informamtion Partition by the exhaustive search
% from probability distirubtions
%
% INPUTS:
% probs: pro... |
c7893093d93069934dd3c06cc316ddefc4906a5a0d9b123e8b0fe0e1b191743a | MATLAB | 2,800 | 63 | function fixed_SNR = interpolate_missing_SNR_trigs(SNR_timings)
% Function interpolate_missing_SNR_trigs fills in missing triggers in the SNR trigger stream.
% There can be arbitrary number of missed trigs, including triggers missed in a raw.
% Assumptions:
% 1. The SNR triggers are produced at a unifo... |
004b4cdcecb617a30a0233a22af49cc8085bd5765a0977dbf3bb661d40138ef5 | MATLAB | 2,810 | 90 | function snr_times = AO_process_ttls(in_folder, result_folder)
fnames = dir(fullfile(in_folder, '*.mpx'));
n_fnames = size(fnames, 1);
if n_fnames == 0
log_msg(result_folder, 'no-mpx', ...
sprintf('No .mpx files found in %s', in_folder));
error('No .mpx files found in %s', in_folder)
end
% JN 2020-0... |
458371ea85fbe428282f05d794651bdb832cf55b0ec3f88377dfbc6e35291709 | MATLAB | 2,815 | 93 | function gramm_2x2_RESP_NSNDEvariation(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);
c... |
1904ed5285050f82b8aaff7018e123dee0a29b1bdf346605671bc3aa08e0ce64 | MATLAB | 2,817 | 49 | function SUBJECT = ASLT1fromM0Processing(SUBJECT, prefix, fast)
% ClinicalASL toolbox 2023, JCWSiero
% Construct T1w image from multi PLD M0 image
% brain extraction on M0 image
system(['bet ' SUBJECT.ASLdir prefix '_M0 ' SUBJECT.ASLdir prefix '_M0_brain' ' -m -f 0.4 -g 0']); % extract brain mask of M0's
system... |
bdd0812d61e8112021f01c0b05437abd46f8bd988784c7f3c906dbd90aa28901 | MATLAB | 2,817 | 75 | %---------------------------------------------------------------%
% This is the main script for get decoding error of animal's %
% current position using rate maps from N' in a trial-by-trial %
% basis -- Wenbo Tang (Jan 05, 2023) %
%-------------------------------------------------------... |
ef534abc68bca95c737308e47e09e7e6ee3e004557f8b16100d92c41c89dee57 | MATLAB | 2,822 | 90 | function events = AO_extract_ttls_from_mpx(fname)
% JN 2019-02-10
% extract TTL events from MPX files
fid = fopen(fname, 'r');
data = fread(fid, 'uchar=>uchar');
fclose(fid);
pre_alloc_size = 30000;
isAnalog = zeros(pre_alloc_size, 1);
ttlnums = zeros(pre_alloc_size, 1);
sampling_rates = zeros(pre_alloc_size, 1);
o... |
b3fcfc9381edec408a3e9571db8741efa46a53e0879f186bba6d9df271022e96 | MATLAB | 2,823 | 89 | function gramm_2x2laminar_line(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM(1:560);
clear Dat... |
cff028be5bdfd53ce83891405e36c4881177268435f99cfe9b6b56be418f2f9d | MATLAB | 2,837 | 62 | function [labels] = getTIFFLabels(path, varargin)
% This is a function for loading tiff labels, whether it be a multipage tiff
% or a folder of individual tiff files. You are expected to provide a path
% to the Point that holds your data. If your Point is a folder that has
% some internal structure more complicated tha... |
9b20d118bed1ac4c4c545b62330d8b87702df4bcfeb712bfd1143b0a17bf69dd | MATLAB | 2,864 | 148 | sb
v_data
plot(t, V)
ylim([-70, 35])
xlim([1.01, 1.135])
% Action potential, membrane currents and intracellular Ca2+
% Nernst potentials
Na_o = data.Na_o; Ca_o = data.Ca_o;
E_k = nernst(K_i, K_o, 1, data);
E_Na = nernst(Na_i, Na_o, 1, data);
E_Ca = nernst(Ca_i, Ca_o, 2, data);
% Fast delayed rectifier K+ cur... |
23730ef2ea3b218f6eab4959b5365aa7b76a901109dc797972826f76c3e5d07c | MATLAB | 2,875 | 71 | %% Create urgency signal
% Oscillations in the higher Beta band (16:30) are taken as indicators of motor preperations
% and are use to constrain our neurally-informed models, the grand-average Beta amplitude
% waveform in the 8 sec ITI was taken (Calculated with dataAnalysis.m) and normalised according
% to the motor... |
e0f0b16ce1c42c06427d4d41e6f79384dbc32d012c30d00c849556af4a3f9fc3 | MATLAB | 2,877 | 95 | function asyncSoundOUT_test2(q,sounds)
send(q,'start');
qout=parallel.pool.PollableDataQueue;
send(q,qout);
S=load(sounds);
sounds=S.sounds_data;
dev=audioDeviceWriter;
dev.Driver='ASIO';
dev.Device='ASIO MADIface USB';
dev.SampleRate=192000;
dev.ChannelMappingSource='Property';
dev.ChannelMapping=1:14;
dev.SupportVari... |
6745b79f03264466cdbb13328ba704a07bf2d240ea5f86754922d95ede4b961e | MATLAB | 2,882 | 67 | function sig = Signal(varargin)
% Signal class constructor.
% Signal(name) constructs a signal with a given name.
% Signal is the base class of all signals (BBN, FREQ,MTF ...etc) .
% Creating a new signal:
%
% Creating a new Main_signal (assuming it's name is NEW_SIGNAL):
% 1. Creating a library with the name : @NEW_S... |
0309cad68b605a3b92bf2e53c0ebce1a39714d62401ac16d928889f6242583ce | MATLAB | 2,888 | 76 | function sig= update_comp_by_index(sig,index,input_method,varargin)
% UPDATE_COMP updates the given componentof the Signal with the given input
% method.
% UPDATE_COMP(SIG,COMP_NAME,INPUT_METHOD,VARARGIN) updates the relevant component
% (according to comp_name) with the given input method ('STATIC_VALUE', 'SWEEP',or
%... |
47b410d3b7d4e0bcbc99e5b23a90aea7c81399b2c2c971f2642b7b160a040800 | MATLAB | 2,889 | 87 | function runTrainingSession(kind)
%RUNTRAININGSESSION opens a GUI to run a detection training session.
% Arguments:
% kind - 'gap' for gap-in-noise detection training [default];
% 'tone' for tone-in-noise detection training.
% Author: Lasse Osterhagen
if nargin < 1
kind = 'gap';
end
switch kind
... |
bb118fe7c97bdd4fd13cee8367a8c07e7574a154511e6070f1c80e7244aa2b81 | MATLAB | 2,889 | 78 | function summary = RELIABILITY_SELECTION(dat_in, varargin)
% dat_in does not acount for time
% dat_in is a cell array of the samples that the function draws from. In a
% sense this is the trials for a given condition of interest or the
% "features" presented. I.e. datin = 1x3cell [eye_1,eye_2,eye_3]
%%% THIS function ... |
7d108777409e7b508e584e9b643e8686ab2cfdf391dc46d1b6095bf99b534edf | MATLAB | 2,907 | 63 | function db1Pulse = PPS_MakePulse(inNSamp, chPType, varargin)
%Utilty function generating a pulse.
%Synopsis:
% DB1PULSE = PPS_MakePulse(INNSAMP, CHPTYPE, [VAR])
%Input:
% -INNSAMP: number of sample of the output pulse
% -CHPTYPE: charater array specifying the type of pulse. Can take the
% following val... |
7e5b2c7918ca0c637200b0fe8facd54028558d1d1eba2a07c7f267d4ed48bb49 | MATLAB | 2,910 | 97 | function res=check_params(varargin)
% res=CHECK_PARAMS(PARAM1,VAL1...) checks the validity for a Basic_line object.
% Checks that PARAM1 field can hold the given VAL1 value and the same for
% PARAM2,VAL2 and so on.
% If all params are legal - returns 1. Otherwise returns 0.
global LINE_REAR_NAMES;
global LINE_LEAR_N... |
fc19e185fc25adbee8e0d68b432491b88ccb2e63d28b5131bc32d4f432a6b52e | MATLAB | 2,911 | 84 | function [X,N_features,featurenames,featureind,coeff]= preprocess_features(X,pars)
N_features=length(X.datapars.featurenames);
featureind=1:X.datapars.N_features;
featurenames=X.datapars.featurenames;
if pars.oldonly %use only WENDLING 2005 features
featurenames=X.datapars.featurenames(X.datapars.oldfeatur... |
4718ed32b30d7240f16e77d2c96b153ba6e6c8496d9b92a096f886bd2d713484 | MATLAB | 2,912 | 73 | classdef ExtendChanSampleFactory < AudioObjectSampleFactory
% Decorator that can be used to extend the number of audio output
% channels of an AudioObjectSampleFactory to the number of output
% channels in use by an AudioPlayer. Those additional audio channels
% will all be zeroed.
% Example: If an AudioObjectSampleFac... |
76a69e46365693ea975207e33c4b4f2bccc2f92fdd26f18ccf40a2c8fed3463a | MATLAB | 2,914 | 74 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <freqSpec: returns the frequency amplitude (or power) spectrum of input timeseries data >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License a... |
65dabc00bdbcdd5ba59a3e3459d0d2003bd2638f48c711f1019d20742e7dd13a | MATLAB | 2,917 | 64 | function [metablock,line_coordinated_channels]=invert_metablock(meta)
% INVERT_METABLOCK invert the metablock in a way that the Trial-duration
% component of each line will be considered when coordinating and building
% the trials table of values for the Metablock.
% [METABLOCK,LINE_COORDINATED_CHANNELS] = INVERT_META... |
535aacb62d1a4db03dd67d062aa4ecae40d0ba8c51de6ec6ce3bd72296dc5049 | MATLAB | 2,923 | 96 | function asyncSoundOUT_test2(q,sounds)
send(q,'start');
qout=parallel.pool.PollableDataQueue;
send(q,qout);
S=load(sounds);
sounds=S.sounds_data;
dev=audioDeviceWriter;
dev.Driver='ASIO';
dev.Device='ASIO MADIface USB';
dev.SampleRate=192000;
dev.ChannelMappingSource='Property';
dev.ChannelMapping=1:14;
dev.SupportVari... |
fac48709f232e680eb30d5a0ab76c8a3f36fbed95011d82b28971567b49ef0a8 | MATLAB | 2,933 | 71 | % MIBI smooth stitching script
% Author: Dmitry Tebaykin
% Contact: dmitry.tebaykin@stanford.edu
%% Necessary parameters
% Provide the XML file path from the run, stitching parameters will be
% extracted automatically. Example: xmlFileName = '180501_Hip_Panel3ug_Final-2b.xml';
xmlFileName = ''; % Leave this blank for ... |
19491a63f73b830c7cf7185a85dffadced5b295f17208ac0fe3567a666f4f74b | MATLAB | 2,947 | 89 | classdef ArduinoDevice < InputOutputDevice
%ARDUINODEVICE establishes a serial connection to an Arduino (Uno).
% Data transmission is realized by 2-byte arrays with the first byte
% specifying the pin involved and the second byte specifying the
% associated value.
% If the class receives data from the Arduino, ... |
6ca8f74a99892244bd0c549838cff6c02000c02cec69d3d654cec60dfe0759a0 | MATLAB | 2,950 | 46 | % Authors : Tatjana Schmitt & Simon Wadle 2019-2022
function time_points = time_points_frames(txt_filename_frames, varargin)
% normalizes frames to real time points in ms and frames
% output is a cell array with time points & frame number of each presented stimulus and
% all start and end times & frames for calcul... |
ea81b1891aff6467d41de4fd555a41915490d79b59bb264b4d584ee310f32017 | MATLAB | 2,953 | 78 | function generatePanels_FigS5_rev(FigS5)
%% READ ME
%% Colormap
figure(150);
colors=flip(FigS5.constants.colormap((1:4),:));
tempMap(1,:)=FigS5.constants.colormap(1,:);%REM
tempMap(2,:)=FigS5.constants.colormap(4,:);%Active Awake
tempMap(3,:)=FigS5.constants.colormap(2,:);%Quiescence
tempMap(4,:)=FigS5.cons... |
fdc317cc2469a418604cd74fe7f74320f45f62dd63fc427da70cc7a6b4bbe5ff | MATLAB | 2,960 | 90 | classdef GapTrainingStimuliGeneratorTest < matlab.unittest.TestCase
% Author: Lasse Osterhagen
properties (Constant)
defaultGapDurMean = .01;
defaultGapDurStd = .002;
defaultStartDelayBounds = [1, 5];
end
properties
% default config
config
defaultGapDurBounds % (constant property ... |
b67704958d71abd5d9de05e1f5cb74a38ae20d6fcaf2517854500b55ef378e95 | MATLAB | 2,962 | 91 | function line=set(line,varargin)
% SET Set Line properties and return the updated object
% Property names are:
%
% Right ear - a String that represents the channel that participate
% in the syntisiesed on the right ear.
% The options are: '1', '2', '3', '4', '3+4', '2+3+4', '1+2+3+4','SILENCE'.
%
% Left ear - a String... |
bb139688214d72ff9d3afebf764aeab572fc15e9d48496c91a8abd1ba50e8699 | MATLAB | 2,967 | 116 | function Wsoc = soc_function(W_initial, rate, desired_SA, gamma, end_exc)
% Code from Vogels et al., 2018, Nature Neuroscience
% By Jake Stroud
%% Create a stability-optimised circuit
Wsoc = W_initial;
% Plot spectrum of W_initial
figure
subplot(2,1,1)
plot(eig(Wsoc),'*');
xlim([-10 10]);
ylim([-10 10]);
xlabel('Rea... |
14d696307cebc4dcd71beb03d449bcc23422baf2ba0579fe6face568a704717d | MATLAB | 2,971 | 77 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <import_RGM: imports GEN4 RespirAct data >
%
% 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 Founda... |
3d883aaa0cae801057c1aa8425cc3116a3d159a937082a9938ff1ab0945a19e3 | MATLAB | 2,974 | 101 | function [ phi_G, Cov_E_p, A_p ] = phi_G_Gauss_AL( Cov_X, Cov_E, A, Z )
%------------------------------------------------------------------------------------------
%PURPOSE: calculate integrated information "phi_G" based on information geometry
% with an augmented Lagrangian method
%
% See Oizumi et al., 2016, PNAS... |
a2f0f1171b574cacefcc55f73eb7f7e6c15de3d07ca2a2ee329080777285620e | MATLAB | 2,976 | 112 | % script to extract betas
%dbstop if error
glm= 'GLM_GUSTO';
task='hedonicreactivity';
list_roi = {'Pirif', 'insula'};
% which contrast
con_list = {'con_0002.nii'; 'con_0003.nii'}; %
con_name = {'reward'; 'neutral'}; %
%% DEFINE PATH
cd ~
home = pwd;
homedir = [home '/OBIWAN'];
for k=1:length(con_list)
... |
b910608d0d77b2e6b0b539284a66a5b721d14559afd7aaffd0d84a32565df31a | MATLAB | 2,984 | 104 | function plot_supp_2(my_axes, S, param, axlabel_flag)
ns_pre = S.ns_pre;
thr = .25;
dset = S.dset;
clear('S');
time_const = 29.997;
rats = 4:8;
days = 22:23;
start_time = .5; % sec after prev_fdb
stop_time = 9; % sec after prev_fdb
start_samp = round(start_time * time_const) + ns_pre;
stop_samp = round(stop_time *... |
f0a53d133dc2555f1a979d49801d1d3723cc1e1d44aa6276715369464d10aa83 | MATLAB | 2,988 | 93 | function [snr_time_fixed, stats] = ...
fix_state_timestamps(method, snr_time, mdp_states, ...
last_idx_before_skip, folder_log)
onset_window = 3600; % 1 hour
if strcmp(method, 'ttrig')
% specific to this method: find points where the ttrig column increased
ts_idx = find(diff(mdp_states.ttrig) > 1e-5) ... |
03dc9b6ea17e90c534f8c07c849a72ba5dbe7fabe91df3b2cfbb519643757b28 | MATLAB | 3,000 | 77 | function C_fitting_lag(datswitch)
load('A_dataload.mat','NE','NM')
switch datswitch % choose between near miss and narrow escape data
case 1
dat = NE;
case 2
dat = NM;
end
name = dat.outcomename;
EEGtime = dat.eegtime;
EEGdat = dat.eegcurve;
... |
404f88e68c461e498c30c7bd6fd7aacdc3a12b4316ef1f6db906b41b218fc7c3 | MATLAB | 3,003 | 79 | function sig= update_comp(sig,comp_name,input_method,varargin)
% UPDATE_COMP updates the given componentof the Signal with the given input
% method.
% UPDATE_COMP(SIG,COMP_NAME,INPUT_METHOD,VARARGIN) updates the relevant component
% (according to comp_name) with the given input method ('STATIC_VALUE', 'SWEEP',or
% 'SEQ... |
31411e41fecf3bac75bad1e842f3c507c066db0fedc285de9a788f062441ef1e | MATLAB | 3,005 | 82 | classdef GapStimulusSampleFactoryTest < matlab.unittest.TestCase
% Author: Lasse Osterhagen
properties(Constant)
gaps = [1, .1, .01, .001];
sFs = [44100, 192e3];
gates = [.001, .0005];
end
methods(Static, Access = private)
function [outSamples, requiredSamples] = applySampleFac(gapDuration, ... |
384d3b40c1c95a4b78c9880a251094773b67dc9211a0bf5ff9880ec08e229f89 | MATLAB | 3,007 | 75 | % Function to get 1 point per y value
% Updated: August 30, 2022
function [dendSkel] = SinglePointBin(dendSkel,dend_lbl,dendCent,dendMax,dendNum,neur_mvmean,neur_idx_avg)
% Determine how large of deviation is permitted
pxldev = 7;
% For each pixel row, keep the point that is closest to the moving mean
... |
18bcbb9a31389e0a155762e4c8f541fbb0d32bed544ec54bc831e156a594da3a | MATLAB | 3,010 | 76 | function [remapped] = mapEmbedding(embedding,sourceEigVecs,destEigVecs)
% mapEmbedding Remaps the matrix of row vectors embedding from the space
% spanned by sourceEigVecs to the space spanned by destEigVecs.
%
% IMPORTANT:
% embedding = matrix whose rows are the points in embedding space
% represented by row ... |
398bd55b365275921e81096ea3742ff8d837bb4686b9b17c4f9e43c69af6726b | MATLAB | 3,013 | 104 | function struct2csv(s,fn)
% STRUCT2CSV(s,fn)
%
% Output a structure to a comma delimited file with column headers
%
% s : any structure composed of one or more matrices and cell arrays
% fn : file name
%
% Given s:
%
% s.Alpha = { 'First', 'Second';
% 'Third', 'F... |
82d3d54cd25630194be38baeb547f3937453f90b8a4b27b6fea9685177b460da | MATLAB | 3,016 | 95 | function [sortIndex,newROICount,firstSort,secondSortID] = chanSort(ECoGchannels,ROI_table,majorROI,minorROI,suppressWarning)
% Sort ECoGchannels by major and minor ROIs
%% Default is to sort first by newROINum, second by oldROINum
if nargin<3 || isempty(majorROI)
majorROI = 'newROINum';
end
if nargin<4 || isem... |
20215fa090f9547b8665c56ad45b0f9a886a004f57a653177bbcdd3c9c969805 | MATLAB | 3,022 | 81 |
clc
clear
close all
load same_or_diff_LDA.mat
% find neurons with at least one matched bin
ind_bins = same_or_diff==1;
ind_neurons = any(ind_bins,2);
n6c = sum(ind_neurons);
disp(['N_Fig06C: ',num2str(n6c)])
% load classification performance as plotted in fig.4A
load xx_108_4_single_e2o_perf
exe2obs_cell = cellfu... |
ab9f1367664d3aa739b2e2802e7349e57c5c80fb2869eedde264fd36981b107e | MATLAB | 3,024 | 99 | %% significance of distance
clear; clc;
%%%% distance in subspace %%%
%load data
load('subspace_position_A.mat');
real_a = sdata;
load('subspace_position_B.mat');
real_b = sdata;
load('permutation_A.mat');
perm_a = sdata;
load('permutation_B.mat');
perm_b = sdata;
% null
distance = struct('A',[],'B',[]);
distance.A ... |
e048e87dd484d5859c83bfb643bfe4eb36fae6e1ccce95930e5f3936b8da04e2 | MATLAB | 3,028 | 133 | function fb_detrend_and_align(DIR,TEMPLATE,ROIS,varargin)
%
%
%
%
%
%
nparams=length(varargin);
fs=22;
per=12;
cut=25;
out_dir='extraction';
save_dir='detrended_aligned';
dat_dir='trace_data';
padding=[0.25 0.750];
if mod(nparams,2)>0
error('Parameters must be specified as parameter/value pairs');
end
for i=1:2:np... |
aba523ec0b3a968819c5f40b2faacb7af07f1292a1be349d32c37f0420456534 | MATLAB | 3,038 | 85 | % Displays MIBI images, calculates and overlays visual mask
function display_segment(handles, pipeline_data, varargin)
%get info for creating base display
[display_point, channel_index, channel_name, channel_counts] = retrieve_view_data_info(handles, pipeline_data);
sfigure(pipeline_data.displayImage);
... |
3d323b6b8c56c4b72d561d33be4dff7612db3a9869b071d22acff5949e1389f9 | MATLAB | 3,052 | 91 | function [P, PE] = gaussianFit( X, Y, opt )
%gaussianFit Gaussian fit
% Makes a 1-D Gaussian fit of a distribution of points
%
% [P,PE] = gaussianFit(X,Y,opt)
%
% X is the x-axis input array (n x 1).
% Y is the y-axis (n x 1) input array. Y can be a (n x m) matrix.
% In this case each column must be an array... |
95b0c420eea47b1429984141c4a8ead0a35c88733fbca0987b9ca47691626e9b | MATLAB | 3,052 | 104 | %%
clear;
clc;
close all;
%% Define parameters
group_name={'group_1' 'group_2'};
dir = 'dir1\';
map_dir = 'map_dir\';
x_pix = 400;
y_pix = 400;
spec_frame = 99;
ext = '.txt';
ext1 = '.xls';
ext_fig = '.fig';
ext_jpg = '.jpg';
% load referece spectrum
load pure_chemicals_... |
4e1799df474c9573887e0dc390a1a82c0169ae7050a208722c280d6632ed7aa0 | MATLAB | 3,054 | 106 | function [q_TPM, q_past, q_joint, q_present] = est_q_table(p_past, p_joint, p_present, N_st, Z, sigma_table, pow_cell)
%-------------------------------------------------------------------------------------------------
% PURPOSE: estimate mismatched probability distribution q from the original probability distribution ... |
eecab9208d4220108849ed92be9fc21356c045ae29235c28202b24b2a65cac77 | MATLAB | 3,058 | 61 | function preprocess_anatomical_prep(fsldir, subjectdir, bet)
k = strfind(subjectdir,'subject');
sub = [subjectdir(k:end),' - '];
clear k
% This is simply helping with the text that will be displayed as the
% function is running. 'sub' is a string with the name of the subject that
% will be printed with every upd... |
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