sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
4e2465abee330c1b60407d10433f49a78e39100b9658800a1c2992434cdf345c | MATLAB | 12,599 | 305 | % ========================================================================
%> @class FixationCrossStimulusTest
%> @brief Class-based unit tests for fixationCrossStimulus.
%>
%> Tests construction, property defaults, type list validation, colour
%> handling, alpha2, lineWidth, showDisk, flash/pulse modes, colour2
%> pro... |
380628e5e3e4ef4c5e8a0187d1efff2acc0999d55fda0e8f7a8a9419e2a9a4c2 | MATLAB | 12,736 | 308 | function [fd,subjects] = calcFD(subjects,subjectpath,options)
% Calculate the fractal dimensionality of a 3D structure.
% Designed to work with intermediate files from FreeSurfer analysis pipeline
% (ribbon.mgz, aparc.a2009s+aseg.mgz, and others).
% Also can use other mgz volume as input (e.g., see 'benchmark folder'... |
62073ac66cd6f45d26a553db3d5734173196e18963b0bef55a859048306d1428 | MATLAB | 12,795 | 244 | % only epochrej using eeglab
function eeglab_only_rejection (subject)
path_file = 'E:\\Srijita\\Data Files\\Behavior Pilots\\2-back\\Unfamiliar-constant (new analysis, Jan 22)\\EEG Analysis\\';
path_save = 'E:\\Srijita\\Data Files\\Behavior Pilots\\2-back\\Unfamiliar-constant (new analysis, Jan 22)\\EEG Analysis... |
b6c18cb427706bbfa3021e98def254e52154f824881bdc4c94f94dcf4855e319 | MATLAB | 12,796 | 290 | % Comparing power between 2 of the followings: baseline, whole epoch, and after dev_on [single subject]
% ver 200901 by poem
%% set parameters (initialize)
clear all;
SL = '\';
FilePath = '';
if isunix
mypath;
FilePath = '~/liang/RS/'; %directory
SL = '/';
end
DR_PBase_setup;
%datasets
PLOT_SET = {
... |
31a501f0d71b28d68b32dc3350ebc269c7633d074a10bcb3f4b830caef68cc09 | MATLAB | 12,813 | 400 | % ========================================================================
%> @brief apparentMotionStimulus, inherits from baseStimulus
%>
%> apparentMotionStimulus is a simple apparent motion stimulus, comprising
%> of a bar which flashes on and off across a series of spatial positions.
%>
%> Copyright ©2014-2022 Ian ... |
390c779b4bf1068399e08d4c92e3088d5e1f507369a627e140cfb87dffe8012c | MATLAB | 12,826 | 269 | % Define the directories and files
clear all
setup_paths;
eye_data_dir = DATA_ROOT;
neural_data_file = 'Mars_TOJ_timestamp.xlsx';
% Get the list of eye movement data files
eye_data_files = dir(fullfile(eye_data_dir, 'Mars_TOJ_eyedata_marker_per_block_matched_list*_r*_b*.csv'));
%% Define the parameters for t... |
e112f53a5e8017d0f845ea1a386039cb76c865875b41b2a1167bd8855f450889 | MATLAB | 12,827 | 406 | %Code from https://www.mathworks.com/matlabcentral/fileexchange/30733-hatchfill
% Neil Tandon. Hatchfill (https://www.mathworks.com/matlabcentral/fileexchange/30733-hatchfill), MATLAB Central File Exchange.
function H = hatchfill(A,STYL,ANGLE,SPACING,FACECOL)
%% HATCHFILL Hatching and speckling of patch objects
... |
e70d266ad0010fc50aca439a9ee2f95456a789408671fa18ed952adb831a7513 | MATLAB | 12,863 | 278 | %% Demonstration of a command-driven setup of an Opticka MOC Experiment.
% Opticka is an object-oriented framework plus optional GUI for the
% Psychophysics toolbox, allowing randomised interleaved presentation of
% parameter-varying stimuli specified in experimenter-relevant values. It
% is designed to work on Linux, ... |
35525fff049caeb8f90e83454c703383260e58fd165896864ab3d04d51011981 | MATLAB | 12,890 | 295 | <<<<<<< HEAD
function this = subsasgn(this, subs, A)
% Subscript assignment for GIfTI objects
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: subsasgn.m 6513 2015-08-05 17:52:13Z guillaume $
swit... |
6dbe324624f1ced1957e932e1a21009dfef046dd2c2afbe844cf2ddffe670444 | MATLAB | 12,900 | 466 | function varargout = boundedline(varargin)
%BOUNDEDLINE Plot a line with shaded error/confidence bounds
%
% [hl, hp] = boundedline(x, y, b)
% [hl, hp] = boundedline(x, y, b, linespec)
% [hl, hp] = boundedline(x1, y1, b1, linespec1, x2, y2, b2, linespec2)
% [hl, hp] = boundedline(..., 'alpha')
% [hl, hp] = boundedline(... |
0a9a5f35cb3b8202acdbfcb090d9355085b5caf2a55c51dbf8012222c1ec9f11 | MATLAB | 12,910 | 315 | % ========================================================================
%> @class PolarBoardStimulusTest
%> @brief Class-based unit tests for polarBoardStimulus.
%>
%> Tests construction, property defaults, type list, custom properties,
%> sf/sf2 spatial frequency, colour/colour2, contrast, mask, phase,
%> direction... |
0fec66f04c2720c7854af4736fd4029bec446e08eed00355b0adf0f21c4a1998 | MATLAB | 12,931 | 292 | function M_final = apply_shifts(Y,shifts,options,td1,td2,td3,col_shift)
% apply shifts using fft/cubic or linear interpolation
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% tensor, a memory mapped file, or a pointer to a tiff stack
% shifts: calculated ... |
b79f2a2af55dd47ccd23078cba31e60914a123f488d1e5e9c90698e3d78ae74a | MATLAB | 12,942 | 279 | %% Demonstration of a command-driven setup of an Opticka MOC Experiment.
% Opticka is an object-oriented framework plus optional GUI for the
% Psychophysics toolbox, allowing randomised interleaved presentation of
% parameter-varying stimuli specified in experimenter-relevant values. It
% is designed to work on Linux, ... |
e1b706703043d008216f890fc02b0cf61043446102c7e2189af8f46f5c491881 | MATLAB | 12,942 | 376 | % ========================================================================
%> @class dotlineStimulus
%> @brief Show lines made of dots
%>
%> Class providing basic structure for dotline (texture) stimulus classes.
%> You can control multiple aspects of the image presentation, and scale
%> images to values in degrees, ro... |
9287142b2aff381542bb2deb8fbe56d47c88f85c186e29c2b52401807bf4f2e9 | MATLAB | 12,963 | 391 | function varargout = ccal(varargin)
% CCAL M-file for ccal.fig
% CCAL, by itself, creates a new CCAL or raises the existing
% singleton*.
%
% H = CCAL returns the handle to a new CCAL or the handle to
% the existing singleton*.
%
% CCAL('CALLBACK',hObject,eventData,handles,...) calls the local
... |
9225e4fd746ed8be7be663b876a8c03f8cbd60aafc7c66fb23af8eeaa986e055 | MATLAB | 12,993 | 537 | function binocularStimulation(in)
% Version 1.13
movieRecord = false;
if ~exist('in','var')
in.stereoMode = 8;
in.distance = 57.3;
in.ppcm = 36;
in.bg = [0 0 0];
in.left = [0.8 0 0];
in.right = [0 0.3 1];
in.type = 'checkerboard';
in.sf = 0.1;
in.tf = 0;
in.flash = 0;
in.anglemod = 0.2;
in.sfmod = 0;
in.... |
b528110e3b02eb454bcdfda449461a5f6ab652fc7779af7dd30755afc2c029c5 | MATLAB | 12,998 | 408 | function [x, infos] = nenmf(V, rank, in_options)
% Nesterov's accelerated non-negative matrix factorization (NeNMF).
% The problem of interest is defined as
%
% min || V - WH ||_F^2 + r(H),
% where
% {V, W, H} > 0 and r(H) is a regularizer.
%
%
% Given a non-negative matrix V,... |
6c4aefe069e625f4dbc1f5112fdc66b48e28fabfeaf9179c034e97c3900afd78 | MATLAB | 12,999 | 412 | function [sY, IN] = nk_PerfStandardizeObj(Y, IN)
% =========================================================================
% FORMAT function [sY, IN] = nk_PerfStandardizeObj(Y, IN)
% =========================================================================
% Standardisation of matrix Y using different types of estima... |
d1eac7eb7dda7a3497fe657b25f042e7a5f702dc99c12b7a67b8a2d8240e14a0 | MATLAB | 13,023 | 400 | % ========================================================================
%> @brief apparentMotionStimulus, inherits from baseStimulus
%>
%> apparentMotionStimulus is a simple apparent motion stimulus, comprising
%> of a bar which flashes on and off across a series of spatial positions.
%>
%> Copyright ©2014-2022 Ian ... |
3212b29938db3a28085721f2ccaa9c1dfbc26505a22cdaac59a773e10bae5d8a | MATLAB | 13,048 | 330 | function [ mW, mP, mR, mSR, mC, W, mPA ] = nk_VisXWeight(inp, MD, Y, L, varind, P, F, VI, decompfl, memprob, procfl, Fadd)
% =========================================================================
% [mW, mP, mR, mSR, mC, W, mPA ] = nk_VisXWeight(inp, MD, Y, L, varind, ...
% P,... |
b6226b13036e7fba5999f2eb4b25d9d819d471b3c544070164e2f88b2f72bc73 | MATLAB | 13,072 | 346 | function [X, istop, itn] = lsqr2( A, B, damp, itnlim, atol, btol, show)
% This function is provided at
% http://www.stanford.edu/group/SOL/software/lsqr.html
% I have made small modifications -- Deng Cai, April/2006
%
%
% function [X, istop, itn] = lsqr2( A, B, damp, itnlim, atol, btol, show)
%
% [ x, istop, ... |
8097680c0508099f8ea2fb3fbc6c795dbdb79734fed21542fe4948523af06f97 | MATLAB | 13,096 | 294 | % Comparing power between 2 of the followings: baseline, whole epoch, and after dev_on [single subject]
% ver 200903 by poem
%% set parameters (initialize)
clear all;
SL = '\';
FilePath = '';
if isunix
mypath;
FilePath = '~/liang/RS/'; %directory
SL = '/';
end
DR_PBase_setup;
%datasets
PLOT_SET = {
... |
e514391f8a00748e43939249d3052b5f0248f8253e921bd2f1f6edbfc89704fe | MATLAB | 13,126 | 441 | function gui_adv(x, y)
%
% This file is needed by FASTICAG
% This is the advanced options -dialog
% @(#)$Id: gui_adv.m,v 1.4 2004/07/27 13:09:26 jarmo Exp $
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Global variables
% Handle to the window
global hf_FastICA_AdvOpt;
% Handles... |
796367a4682e7af6e052afe36732849c411a3428f24014ae3bb1ffb302a46dfb | MATLAB | 13,153 | 328 | function [c, s, options] = deconvolveCa(y, varargin)
%% infer the most likely discretized spike train underlying an fluorescence trace
%% Solves mutliple formulation of the problem
% 1) FOOPSI,
% mininize_{c,s} 1/2 * norm(y-c,2)^2 + lambda * norm(s,1)
% subject to c>=0, s>=0, s=Gc
% 2) constrained FOOPSI... |
09886a78dbb436e8c4a4564608af1abcb184ce30df13a48a85ec8f6b4b19b6ce | MATLAB | 13,185 | 318 | % ========================================================================
%> @class DotlineStimulusTest
%> @brief Class-based unit tests for dotlineStimulus.
%>
%> Tests construction, property defaults, type/interpMethod lists,
%> itemSize, itemDistance, phase, direction, forceOrthogonal, useEven,
%> colour2, contrast... |
74e381919ce4112886cb4757e6e18197bfda58dd202cc424228539c3021d8a01 | MATLAB | 13,197 | 351 | % For any classifier code below, there's no error as i'm pulling a set
% group of cells each time. Final output of the values as is are in an
% array called day_pct for each chunk; reformated into "viewer" to make
% copy/paste easier.
clear
load('ProcessedData\tables_compiled.mat');
%% calculate sparsness for ... |
7c6695f309298279e9f7b3d4359f9657e2d9f3256803196e35cbdf7671cb78e1 | MATLAB | 13,259 | 397 | function icaplot(mode, varargin);
%ICAPLOT - plot signals in various ways
%
% ICAPLOT is mainly for plottinf and comparing the mixed signals and
% separated ica-signals.
%
% ICAPLOT has many different modes. The first parameter of the function
% defines the mode. Other parameters and their order depends on the
% mode. ... |
4ea80666345e7006012eff83f79d2cd695c8484b6aedcb3d83b183ebdea2ffa5 | MATLAB | 13,269 | 336 | classdef SpcCutter < MClust.Cutter
%
% Select clusters from those generated by KKwik
%
% Version control: ADR-2013-12-12
properties
figHandle_AvgWV = [];
figHandle_ISI = [];
whoHasFocus = [];
whoHasComparison = [];
rootCluster = [];
C = [];
... |
aa02ff9d77f2c8fd3cb0798c91c6895dbd20b5cc544a364149489ab78692026f | MATLAB | 13,447 | 404 | %% FUNCTION MultiSource_LogisticR
% Incompletet Multi-Source Learning with Logistic Loss (optimization)
% This function is not intended to directly called by users.
% See the Logistic_iMSF function.
%
%% OBJECTIVE
% see manual.
%
%% INPUT
% A_Set: {n * d} * t - input. The cell array of data. Each cell should ... |
9840d28df0a8dc9c29afffc725957c09194f36c9c9ccb6ba91d3072b80e7e69b | MATLAB | 13,477 | 348 | function mediansplitBI_PSTHs(EventTypes,partition,parttags,group,patgr)
%MEDIANSPLITBI_PSTHS Peri-event time histogram (PSTH) of units separated by median bursting index
% MEDIANSPLITBI_PSTHS(EventTypes,partition,parttags)
% generates average PSTH plots (with standard error) for low- and
% high burstin... |
d8e2dabd721b3778e7d2e5133bd3658abed5f213a6c619d621285f1622359cd3 | MATLAB | 13,524 | 395 | % ========================================================================
%> @brief draw fixation cross from Thaler L, Schütz AC,
%> Goodale MA, & Gegenfurtner KR (2013) "What is the best fixation target:
%> The effect of target shape on stability of fixational eye movements."
%> Vision research 76, 31-42 <http://... |
889fcf296063a907a1fb2e1d4c390e69b1f37e86e325394a431972b0a5d6c793 | MATLAB | 13,548 | 395 | % ========================================================================
%> @brief draw fixation cross from Thaler L, Schütz AC,
%> Goodale MA, & Gegenfurtner KR (2013) "What is the best fixation target:
%> The effect of target shape on stability of fixational eye movements."
%> Vision research 76, 31-42 <http://... |
766256461cb6593eadbb303e25f6bead8d59fd020265fd1f9ef210b65f27bb53 | MATLAB | 13,677 | 381 | function [ Res, IN ] = nk_SimulateML(IN, axes)
% =========================================================================
% FORMAT function [ R, P ] = nk_SimulateML(IN)
% =========================================================================
% This function is part of the NeuroMiner machine learning library.
% It ... |
0d5228a299e649bd83d380c364a857e87d50be3a885929246d76fa309680c1f3 | MATLAB | 13,695 | 430 | function result=rapca(data,varargin);
%RAPCA is a 'Reflection-based Algorithm for Principal Components Analysis'.
% It is resistant to outliers in the data. The robust loadings are computed
% using projection-pursuit techniques and reflections.
% Therefore RAPCA can be applied to both low and high-dimensional data s... |
835a3dc5868cad25bc38aaa5d9a820c7edf758158ea6f4cac2430bd7fe5ae631 | MATLAB | 13,732 | 362 | function [GD, MD, DISP] = nk_GridSearchHelper(GD, MD, DISP, i, nclass, ngroups, CV1PerfData, CV2PerfData, models)
global VERBOSE MULTI CV BATCH SVM MODEFL W2AVAIL RAND MULTILABEL RFE SAV
%%%%%% TRANSFER RESULTS TO GD :
if SAV.savemodel && (exist('models','var') && ~isempty(models))
MD{i} = models;
end
%% CV1 te... |
ae82881bb0d87cc16554f91cb531f2b67b9a2f3cb42d31f8b5107bd24f7b7bf3 | MATLAB | 13,757 | 377 | %% IT Neuron Archetype Analysis - Main Script
% This script consolidates ParTI fitting and 3D visualization for
% cross-species IT neuron archetype analysis (Figure 2G-I, K, O-P, S3A-B)
%
% Prerequisites:
% - ParTI toolbox: https://github.com/AlonLabWIS/ParTI (put this on the path)
% - CSV exports from R notebook:... |
26c301454a718e0cd8dfe3110b39496e189599200e0694d7d8b7b51ca2b96c75 | MATLAB | 13,789 | 268 | function map = magma(n)
% Returns the "magma" colourmap.
if nargin < 1
n = size(get(gcf,'Colormap'),1);
end
values = [
1.46159096e-03 4.66127766e-04 1.38655200e-02
2.25764007e-03 1.29495431e-03 1.83311461e-02
3.27943222e-03 2.30452991e-03 2.37083291e-02
4.51230222e-03 3.49037666e-03 ... |
30af4e51d61d3ad1af76d7068ef5378305b158f9ceb6bb241aaa9229cf7353a3 | MATLAB | 13,791 | 268 | function map = plasma(n)
% Returns the "plasma" colourmap.
if nargin < 1
n = size(get(gcf,'Colormap'),1);
end
values = [
5.03832136e-02 2.98028976e-02 5.27974883e-01
6.35363639e-02 2.84259729e-02 5.33123681e-01
7.53531234e-02 2.72063728e-02 5.38007001e-01
8.62217979e-02 2.61253206e-0... |
1ef9b999c2198110896d8f493afb529900c29ae646ba5e2b1442d30999166e51 | MATLAB | 13,793 | 268 | function map = inferno(n)
% Returns the "inferno" colourmap.
if nargin < 1
n = size(get(gcf,'Colormap'),1);
end
values = [
1.46159096e-03 4.66127766e-04 1.38655200e-02
2.26726368e-03 1.26992553e-03 1.85703520e-02
3.29899092e-03 2.24934863e-03 2.42390508e-02
4.54690615e-03 3.39180156e... |
7eedb6f2f361765a2e4e5d4488a20dc851150a69624975e2c0893fde7414a321 | MATLAB | 13,793 | 597 | function [U,S,V] = randpca(A,k,raw,its,l)
%PCA Principal component analysis
%
%
% [U,S,V] = PCA(A) constructs a nearly optimal rank-6 approximation
% USV' to C(A), where C(A) refers to A after centering its
% columns, using 2 normalized power iterations, with block
% size 6+2=8, ... |
4734f15dae0b9f63cdaa68b4887016c303d488863c15095730dd69525e3ce784 | MATLAB | 13,794 | 372 | function [act, datacontainer, inp ] = nk_ManageDataContainers(act, inp, datacontainer, parentstr)
nk_PrintLogo
if inp.oocvmode
containerstr = 'OOCV ';
else
containerstr = 'Training/CV ';
end
% check whether an alternative label was used in one of the locked analyses
if inp.oocvmode && datacontainer.labels_kno... |
f87a04ce2c7eb3e948232b32e41b491e1bfaf4d78145baf8ca2c7675c7c19aaa | MATLAB | 13,882 | 274 | % Comparing power between 2 of the followings: baseline, whole epoch, and after dev_on
%This version: 200903 by poem
%% set parameters (initialize)
clear all;
SL = '\';
FilePath = '';
if isunix
mypath;
FilePath = '~/liang/RS/'; %directory
SL = '/';
end
DR_PBase_setup; %load setup file
MN = 'motion... |
cb5831c2778914a62fd934b8276710802e7c1abbf30d437ec62fc48083441ed0 | MATLAB | 14,038 | 438 | function ButtonName=MFquestdlg(Pos,Question,Title,Btn1,Btn2,Btn3,Default)
% MFQUESTDLG Question dialog box.
% -----------------------------------------------------------------------
% --------------------- Modified Function Help ----------------------
% �MFquestdlg� is a simple modification of �questdlg� which enabl... |
26692364a422e083e3ae6459d8e80562f74165ec92459b94de930270e95a6fc2 | MATLAB | 14,061 | 273 | % ========================================================================
%> @class HSMOption2Test
%> @brief Class-based unit tests for stateMachineTree (Option 2: node tree).
%>
%> Converted from the legacy function-based hsmOption2Test.m to use
%> MATLAB's matlab.unittest.TestCase framework. Each original TEST secti... |
fbec9626fce8c77b690bc963320f5efe574ac041f14c8128956a171a1e2ca320 | MATLAB | 14,194 | 367 | % =========================================================================
% = CLASSIFICATION PLOTS =
% =========================================================================
function handles = display_classplot_oocv(h, handles)
% Prepare axes
warning off
axes(handl... |
de6a16a0da5890a74223513a1843356f9f1a33cd2d2458aa0d669c4e674ffd60 | MATLAB | 14,200 | 354 | %DOT COLOUR state configuration file, this gets loaded by opticka via runExperiment class
% The following class objects (easily named handle copies) are already
% loaded and available to use. Each class has methods useful for running the task:
%
% me = runExperiment object
% s = screenManager
% aM = audioManager... |
662ddf09f40ba093ac9b583603b5417f447f02855427fab080b56f81c8be2c5c | MATLAB | 14,252 | 396 | function [noise_data refscan_data image_data]=datapack_VB(twix_obj,varargin)
noise_data=[];
refscan_data=[];
image_data=[];
%setting up defaults
file_prot='meas.asc'; %default protocol file name
file_raw='meas.out'; %defualt rawdata file name
flag_debug=0;
flag_debug_file=0;
output_stem='meas';
flag_scan_mdh_o... |
a74927d32b6b8634db120cf9ed9b5d49edd5248fd0b9b3c5706fa02d5fa0ac24 | MATLAB | 14,372 | 472 |
function [data, timestamps, info] = load_open_ephys_data(filename)
%
% [data, timestamps, info] = load_open_ephys_data(filename)
%
% Loads continuous, event, or spike data files into Matlab.
%
% Inputs:
%
% filename: path to file
%
%
% Outputs:
%
% data: either an array continuous samples (in microvol... |
493b579b64a64d69d323a01077710f2d4a38f5048dc90b8ac42d2f5aae98c732 | MATLAB | 14,382 | 328 | % VEPTest protocol. DOESN'T use the eyetracker, runs a polar grating with
% different direction and contrast, present a fixation cross to guide the
% subject's eye's to be stable.
% fixed times for the state machine (see below)
fixTime = 0.5;
stimTime = 2;
ISITime = 1.9;
%=============================================... |
513c8da1b0f3a196914df990788da260b89c035c7a06bfc3cd923771f4b3c57b | MATLAB | 14,483 | 453 | % ======================================================================
%> @brief Display++ Communication Class
%>
%>
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ======================================================================
classdef plusplusManager < optickaCore
propert... |
ec87146ee782d4a3ece2c5b4623f803025d323715f50376e3e2d49c4866c5ea9 | MATLAB | 14,505 | 324 | % ========================================================================
%> @class PolarGratingStimulusTest
%> @brief Class-based unit tests for polarGratingStimulus.
%>
%> Tests construction, property defaults, type list validation, custom
%> properties, colour2/baseColour handling, spiral/arc parameters, and
%> pha... |
a1478a944c338851adb2a0218fc91099df982e1a83f8e23713097d86d888c2ff | MATLAB | 14,512 | 285 | %% generate new tables compiled with behavior values included
clear
load('InputParameters.mat');
load('PreProcessed.mat');
load('Behavior_TraceTable.mat');
% expected frame count; used to weed out missing trials at one point
max_frames = (inputValue.trialTrace_Pre*60 + inputValue.trialTrace_Post*60);
% other pre-loop ... |
86146988da28b5ba8b5ef79bb7aff2aa507d13476c2cb4ae9c4915cd6bed51d9 | MATLAB | 14,533 | 558 | function tree(objectorder,heights)
%TREE creates a tree in which the leaves represent
% objects. The vertical coordinate of the junction
% of two branches is the dissimilarity between the
% corresponding clusters (maximal 30 objects allowed).
%
% The algorithm is fully described in:
% Kaufman, L. and Rousseeu... |
342aca26d4ad2381bdf5ab26fab1c9d7d3ea6cb3e0e932f638ebee2ee02e65d5 | MATLAB | 14,540 | 224 | function gui_help(which_help)
%
% Used by FASTICAG
% All the help texts and title used by GUI are stored here.
% Make changes here.
% Also displays the helpwindow with the selected text
% @(#)$Id: gui_help.m,v 1.6 2005/10/19 13:05:34 jarmo Exp $
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
91ef182c7a3c894991caf31fd1b21eb072f0a254759cc5ad21de20bb428da812 | MATLAB | 14,645 | 288 | %% generate new tables compiled based on behavior cutoff for motion
clear
load('InputParameters.mat');
load('Behavior_TraceTable.mat');
load('PreProcessed.mat');
% expected frame count; used to weed out missing trials at one point
max_frames = (inputValue.trialTrace_Pre*60 + inputValue.trialTrace_Post*60);
% other pre... |
577683e14fe3d211aeda986f8c80f954fe931596a533702b876444ef79fc5896 | MATLAB | 14,687 | 420 |
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ========================================================================
%> @brief single grating stimulus, inherits from baseStimulus
%> GRATINGSTIMULUS single grating stimulus, inherits from baseStimulus
%> The current properties are:
... |
685fc726b43b210e794476a622a053ee452e82f3d2ade4f1805285deb8997db8 | MATLAB | 14,706 | 483 | function result = cvRsimpls(x,y,kmax,rmsecv,h,k)
%CVRIMPLS calculates the robust RMSECV (root mean squared error of cross-validation) curve
% for RSIMPLS or the robust RMSEP(root mean squared error of prediction) value in a fast way.
% The R-RMSECV curve can be used to make a selection of the optimal number of
% com... |
ab857a2c897379e3d44d076ee967e274d1517608d8c669139c9d64f3eba56230 | MATLAB | 14,725 | 391 | function spik_phas_extraction(sess2analyse,win,freqs, fr_names,PCdir,EventTypes,SubEventTypes,varargin)
%SPIK_PHAS_EXTRACTION Phase values associated with spiking
% SPIK_PHAS_EXTRACTION(sess2analyse,win, freqs, fr_names,PCdir,EventTypes,SubEventTypes,...)
% -Extracts phase values associated with spiking activity ... |
f2d3d1cbaf9c6df9d88ec7b95b8b9491e5bca10a29f47b755651b7bb82b02ec6 | MATLAB | 14,790 | 422 | % ========================================================================
%> @class aprilTagStimulus
%> @brief Texture-backed binary checkerboard / AprilTag-style stimulus.
%>
%> This stimulus builds a binary MATLAB array either from a user-defined
%> `patternMatrix` or by randomly generating 0/1 values for `rows` x
%... |
bdf15773af6f038cfeb767fd1a3089e7bd4bde7af57e8440853fdd7cea2de59f | MATLAB | 14,795 | 381 | function Res = nk_ImReliefVisCVGrid(TempDir, CV, FEATSEL)
if ~exist('TempDir','var') || isempty(TempDir)
RootDir = spm_select(1,'dir','Select IMRelief root directory');
if isempty(RootDir), reutrn; end
end
[niy, njy] = size(CV.TrainInd);
[nix, njx] = size(CV.cvin{1,1}.TrainInd);
switch FEATSEL.BINMOD
case... |
eb46e050851b35921f206b8840cb5e82c324ea699fec24b92ebfb71c9a4fc00b | MATLAB | 14,846 | 413 | function [Z, ccaEigen, ccaDetails] = cca(X, Y, EDGES, OPTS)
%
% Function [Z, CCAEIGEN, CCADETAILS] = CCA(X, Y, EDGES, OPTS) computes a low
% dimensional embedding Z in R^d that maximally preserves angles among input
% data X that lives in R^D, with the algorithm Conformal Component Analysis.
%
% The embedding Z is co... |
8a2f7d0ecf92fa7a851bda94bbdae1d0f785e849ba13850ffd14eeb2228e6ad1 | MATLAB | 14,901 | 336 | % FNIRS protocol. DOESN'T use the eyetracker, runs a polar grating with
% different conditions, but we do present a fixation cross to guide the
% subject's eye's stable.
%
% me = runExperiment object ('self' in OOP terminology)
% s = screenManager object
% aM = audioManager object
% stims = our list of stimuli (m... |
c75a16543bf2073c299144856ff1767fcc55b797fdc54ff6f06e5f202966767c | MATLAB | 14,912 | 360 | function Task_SSRT
%TASK_SSRT Stop signal reaction time task for Parkinson patients
%%%%% AIMS %%%%%
% The task uses a buttonbox which has 3 buttons, a monitor, a
% lightsensor, and a trigger output. The participant has to press two
% buttons in the same order as it is presented in the cue. After the
% keypre... |
899a3987dc59d092b94349636a660303e3b4146258619b05a0845831e0fbe2dd | MATLAB | 15,021 | 338 | % FIXATION ONLY state configuration file, this gets loaded by opticka via
% runExperiment class
%
% This task only contains a fixation cross, by default it uses
% stims.stimulusTable (see below) to randomise the position of the timulus
% on each trial. This randomisation is dynamic, and not saved in any data
% stream;... |
9bdcbbd5087de8d9516b57a15ba934401470fd4368c791a1da213de7b1f8ad5c | MATLAB | 15,031 | 338 | % FIXATION ONLY state configuration file, this gets loaded by opticka via
% runExperiment class
%
% This task only contains a fixation cross, by default it uses
% stims.stimulusTable (see below) to randomise the position of the timulus
% on each trial. This randomisation is dynamic, and not saved in any data
% stream;... |
728e776b2a357b85d9a6496e936f2379f386aeee599236370ed80a88e066fe4e | MATLAB | 15,057 | 427 | clear
load('ProcessedData\tables_compiled.mat');
%% classifier code; runs on increasingly larger random subsets of cells
% % reorg main table if needed
% re_org = vertcat(tables_compiled{:});
% tables_compiled = cell(1,1);
% tables_compiled{1,1} = re_org;
tic
% run within days by iter; params for number of... |
efcc3788315bb43bdf8e97011478a940bc2dd01198d510503c0eb27f21a157ef | MATLAB | 15,110 | 406 | function out = ABA_CTRL_batch(data_path,varargin)
% inputs
p = inputParser;
p.addRequired('data_path',@(x) exist(x,'dir'));
p.addParameter('upload',[],@(x) exist(x,'dir'));
p.addParameter('run',true,@(x) islogical(x) || isnumeric(x));
p.addParameter('include',{},@(x) ischar(x) || iscellstr(x));
p.addParameter('overwrit... |
376dfcb80f6e62a49e7be774a9c707c1f7fd62d29101b31080c09bbfd1131448 | MATLAB | 15,151 | 448 | % ========================================================================
%> @brief Arduino Manager > Connects and manages arduino communication. By
%> default it connects using arduinoIOPort (much faster than the MATLAB
%> serial port interface) and the adio.ino arduino sketch (the legacy
%> arduino interface by Math... |
55e27638ed9161254552bcc5fef568aa995059c832fa04e063fdd43f9e43d757 | MATLAB | 15,155 | 437 | % ========================================================================
%> @brief procedural disc stimulus, inherits from baseStimulus
%> DISCSTIMULUS procedural disc stimulus, inherits from baseStimulus
%>
%> See CreateProceduralSmoothedDisc for the stimulus details
%>
%> Copyright ©2014-2022 Ian Max Andolina — rel... |
0e60827e5db97951b7d0b6a27e83fe4a8fa1b675e31688652cb9a81fe88c3ee8 | MATLAB | 15,202 | 595 | <<<<<<< HEAD
function [vol, M, mr_parms, volsz] = load_mgh(fname,slices,frames,headeronly)
% [vol, M, mr_parms, volsz] = load_mgh(fname,<slices>,<frames>,<headeronly>)
%
% fname - path of the mgh file
%
% slices - list of one-based slice numbers to load. All
% slices are loaded if slices is not specified, or
... |
5c3cc681da608dac018ede3d96657523c1223bd97db547873b5ee62fc3604150 | MATLAB | 15,236 | 440 | % ========================================================================
%> @brief procedural disc stimulus, inherits from baseStimulus
%> DISCSTIMULUS procedural disc stimulus, inherits from baseStimulus
%>
%> See CreateProceduralSmoothedDisc for the stimulus details
%>
%> Copyright ©2014-2022 Ian Max Andolina — rel... |
a666bda04776ca24f3852d6f61bcf012b97375795644322d3b47ff97017ef10f | MATLAB | 15,281 | 480 | classdef audioManager < optickaCore
% AUDIOMANAGER Connects and manages audio playback, set as global aM from runExperiment.runTask()
properties
%> device ID as returned from PsychAudio
device = []
fileName char = ''
numChannels double = 2
frequency double = 44100
lowLatency logical = true
latencyLe... |
f83ddac1f1bd6d5fab21293413449ca0b131934524d7f742d6526cd77702245e | MATLAB | 15,312 | 446 | function [imData,sizx,sizy]=smod_bigread2(varargin)
%reads tiff files in Matlab bigger than 4GB, allows reading from sframe to sframe+num2read-1 frames of the tiff - in other words, you can read page 200-300 without rading in from page 1.
%based on a partial solution posted on Matlab Central (http://www.mathworks.com/m... |
3373757b6f7acf2fd2735d1ec4352f64743da3e77a962a8f7f50c1d2612c8488 | MATLAB | 15,387 | 277 | %power spectra cross subjects (just plotting, no computation)
%merge dipole and spectra (for slide)
%run after DR_PlotClustPBase and DR_PlotClustCompPowerDipole
%mostly base on RS_powbase
%This version: 200903 by poem
%% set parameters (initialize)
clear all;
SL = '\';
FilePath = '';
if isunix
mypath;
... |
4f41334ffeccc50cd9f5771888b85e2658010fc9e8a9b958371a59ed7176ca65 | MATLAB | 15,430 | 368 | %DOT COLOUR state configuration file, this gets loaded by opticka via runExperiment class
% The following class objects (easily named handle copies) are already
% loaded and available to use. Each class has methods useful for running the task:
%
% me = runExperiment object
% s = screenManager
% aM = audioManager... |
d24cfd70e61d551f07a6afb4587af57accd05dfbb745a8f648e4461241cbb4f8 | MATLAB | 15,449 | 404 | function SubSets = nk_CreateSubSets(Y)
global CV RAND RFE MULTI MODEFL MULTILABEL VERBOSE PREPROC STACKING
if VERBOSE && RFE.Filter.flag, fprintf('\n\nCreate feature subsets'); end
[nperms, nfolds, nvar] = size(Y.Tr);
% Do we have a multi-label situation?
if MULTILABEL.flag
if isfield(MULTILABEL,'sel')
n... |
d8d261be5dcbaaac7aab3fab84575418f94adc94c60e0325239d547d87bcb6d9 | MATLAB | 15,449 | 416 |
function condSequence = carryoverCounterbalance(numConds,cbOrder,reps,omitSelfAdjacencies)
%
%When using this function/code in academic research, please cite:
%Brooks, J.L. (2012). Counterbalancing for serial order carryover effects in
%experimental condition orders. Psychological Methods.
%
%Creates a serial-o... |
6be6e9e481ead76dde38d75e1a1d864e23d723a6da3c424ac84ed0a4fa8d2569 | MATLAB | 15,450 | 422 | function obj = subsasgn(obj,subs,varargin)
% Subscript assignment
% See subsref for meaning of fields.
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging
%
% $Id: subsasgn.m 7147 2017-08-03 14:07:01Z spm $
switch subs(1).type
c... |
33606f81e94722bd598f1e4329dc388c5316c5276d35d5baa57ec40a4a33edba | MATLAB | 15,516 | 269 | function MBM = mbm_main(MBM)
% mbm_main is the main function of MBM toolbox which performs MBM analysis
%
%% Input:
% MBM - Structure
% MBM.maps - Structure containing maps. Input fields are:
% MBM.maps.anatListFile - Character vector.
% ... |
5bb6ea761f1b3f1fa58d8feb568d6aba701ece9c5d341a7f7c28277604566540 | MATLAB | 15,560 | 428 | function [ Res, IN ] = nk_SimulateML3(IN, axes)
% =========================================================================
% FORMAT function [ R, P ] = nk_SimulateML(IN)
% =========================================================================
% This function is part of the NeuroMiner machine learning library.
% It... |
b0d7722b860e0430605a868e3e8ca319d24072565b6ddbb1d18f97a394c70c38 | MATLAB | 15,586 | 433 | % ========================================================================
%> @brief target inducer stimulus, inherits from baseStimulus
%>
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ========================================================================
classdef targetInducerStimu... |
577899d14e77cf3f318bd385b825f76bdba4c6ee2595968962b2715473886fae | MATLAB | 15,588 | 192 | function [RawData, AnalysisRegions, Correlograms, InjuryIndicies, ProcessedData, RecordingMetrics, plotProps] = analyzeRecordingPlxFile(plxFileName,sw,plotProps);
%This function initialized output folders and sequentially calls the
%functions to process and label the data, then generate and classify
%correlograms, t... |
ec1591fc2e56c9302b131b358c7633c886e904f44ed83238811c0cd65319590e | MATLAB | 15,819 | 329 | function handles = display_tablegenerator(handles)
if ~isfield(handles,'PerfTabWin')
WinTag = 'PerfTabWin';
h = findobj('Tag',WinTag);
if isempty(h)
handles = init_fig(handles, WinTag);
else
handles.PerfTab.Win = h;
end
end
h = handles.PerfTab.Win ;
set(0,'CurrentFigure',h)
functio... |
4195d09c9473419a89ff11fb3fea1c0cb500352dfa989c281147a51ada94c2c5 | MATLAB | 15,831 | 325 | %{
----------------------------------------------------------------------------
This file is part of the Sanworks ArCOM repository
Copyright (C) 2016 Sanworks LLC, Sound Beach, New York, USA
----------------------------------------------------------------------------
This program is free software: you can re... |
c47c78ea3e258e46d7d52585db8f1e74f56a2c8e977bcff7a1f3ee1d68761f39 | MATLAB | 15,863 | 505 | function [result] = writeNexFile(nexFile, fileName)
% [result] = writeNexFile(nexFile, fileName) -- write nexFile structure
% to the specified .nex file. returns 1 if succeeded, 0 if failed.
%
% INPUT:
% nexFile - a structure containing .nex file data
%
% SOME FIELDS OF THIS STRUCTURE (VERSIONS ETC.) ARE N... |
b086a9babcf202152a984844999bf03863d57fc1e7d5e69f305185133648ab76 | MATLAB | 15,869 | 495 | function [status, paramstr] = nk_SetupGlobalVariables(dat, act, dispflag, varind)
global ...
PREPROC ...
PARMODE ...
SVM ...
RFE ...
CMDSTR ...
MULTI ...
SAV ...
GRD ...
MODEFL ...
SCALE ...
CV ...
RVM ...
RAND ...
VIS ...
MKLRVM ...
DATID ...
SPM5VER... |
ab42ad246a310761f636f08b0449a5116b1a05006b92c0812cdc625a6fa23a6e | MATLAB | 15,904 | 333 | % Comparing power between 2 of the followings: tonic, mixed, and phasic
% This version: 200905 by poem
%% set parameters (initialize)
clear all;
SL = '\';
FilePath = '';
if isunix
mypath;
FilePath = '~/liang/RS/'; %directory
SL = '/';
end
DR_PBase_setup; %load setup file
MN = 'motionless';
p_val ... |
81b9c6609d4e095f93e41d76efd99308a0fd4da217f0f84c48fd8b4c1bccb5ef | MATLAB | 15,941 | 351 | % =========================================================================
% = MODELPERF PLOT =
% =========================================================================
function handles = display_modelperf(handles)
multfl = false;
predind = get(handles... |
f12b7ff94990d22d445e108cbe43a8cc913b241077d5d3b1e6feb76a8701fb97 | MATLAB | 15,961 | 433 | %% GRAPH SIGNAL PROCESSING ANALYSIS OF SOUND PROCESSING IN THE COCHLEA
% Melia E. Bonomo, Santiago Segarra, Robert M. Raphael
% Rice University, 2026
% This code is freely distributed under the GNU General Public License.
% http://www.gnu.org/licenses/gpl-3.0.html
% PATIENT GROUPS
% 32 patients spread across 7 l... |
0789b608506323d39a850b8e7a2070d080a582b5a5f30f11ea4c6ab480b8f081 | MATLAB | 15,974 | 378 | % =========================================================================
% FORMAT param = nk_MLI_config(param)
% =========================================================================
% NeuroMiner menu configurator for the interpretation of model predictions
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
9d497920a5f4852bd7dced6e0dd2f25255de700eef9eb71809c6120f61f5a8fc | MATLAB | 16,003 | 459 | % ========================================================================
%> @brief dotsStimulus simple variable coherence dots stimulus, inherits from baseStimulus
%>
%>
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ====================================================================... |
5a043e4034f5076de5dbc6f518c2000284afaa86a6db772bdbf8cd6a380f3e60 | MATLAB | 16,036 | 459 | % ========================================================================
%> @brief dotsStimulus simple variable coherence dots stimulus, inherits from baseStimulus
%>
%>
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ====================================================================... |
2bb7c4a544ce7e23138dd6f5bf3e5d48452232a8a38c27f31cbea93c1d44e299 | MATLAB | 16,040 | 507 | classdef timeLogger < optickaCore
%TIMELOGGER Simple class used to store the timing data from an experiment
% timeLogger stores timing data for a taskrun and optionally graphs the
% result.
properties
timer = @GetSecs
verbose = true
stimStateNames = {'stimulus','onestep','twostep'}
t = struct('vb... |
73ca610467b414e02e00e63f7af0ecb9f39069258b7a83729696487f748c6772 | MATLAB | 16,070 | 407 | % =========================================================================
% function Predict = nk_PredictData(F, W, TR, TRInd, dTRLabel, ...
% CVD, CVDInd, dCVDLabel, ...
% TS, dTSInd, dTSLabel, ...
% mTS... |
0e77d813bfe224bb356264bb6a31631baa2e68fc77e0208f5d31b0e46a6e8134 | MATLAB | 16,223 | 428 | function varargout = nk_OOCVDataIO(varargin)
% NK_OOCVDATAIO MATLAB code for nk_OOCVDataIO.fig
% NK_OOCVDATAIO by itself, creates a new NK_OOCVDATAIO or raises the
% existing singleton*.
%
% H = NK_OOCVDATAIO returns the handle to a new NK_OOCVDATAIO or the handle to
% the existing singleton*.
%
% ... |
537245dc491db678af32e232a13af4dbd7c508a428d422afb95c82e0ec99ba88 | MATLAB | 16,295 | 479 | % ========================================================================
%> @brief ndotsStimulus limited lifetime coherence dots stimulus
%>
%>
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ========================================================================
classdef ndotsStimulu... |
bcfa33f09edd8fbffa8bede69724c5b347b9a3b18d6da83024499668a42215f3 | MATLAB | 16,295 | 479 | % ========================================================================
%> @brief ndotsStimulus limited lifetime coherence dots stimulus
%>
%>
%>
%> Copyright ©2014-2022 Ian Max Andolina — released: LGPL3, see LICENCE.md
% ========================================================================
classdef ndotsStimulu... |
711fbf28629606d9be716fc1aedf5a1dcea90ed1503f506c384ec56291a276d5 | MATLAB | 16,353 | 364 | % FIXATION TRAINING: Protocol presents a pulsing fixation cross with a
% stimulus in a loop to train for fixation. stims should contain 2 stimuli:
% stims{1} is a attention grabber, stims{2} is the fixation cross. Adjust
% stimulus sizes and eyetracker setting values over training to refine
% behaviour. You can use the... |
e65b22a42048a36c609d61a805634242a8749a55104a33d49a7230107cc112fb | MATLAB | 16,436 | 367 | %component maps, dipoles and power spectra in a cluster
%ver 2009/01
%% set parameters (initialize)
try
close(4001);
end
try
close(4002);
end
try
close(4003);
end
try
close(4004);
end
try
close(4009);
end
clear all;
SL = '\';
FilePath = '';
if isunix
mypath;
FilePath = '~/liang/';... |
dc17dd8672c361c3e24365f1e59453717a2707198bb5a6446e33a95313588c78 | MATLAB | 16,517 | 378 | function [SVM, act] = nk_Model_config(SVM, TrainParam, parentstr, varind, act)
global NM EXPERT
d = nk_GetParamDescription2(NM,TrainParam,'GridParam');
if (isfield(NM,'TrainParam') && isfield(NM.TrainParam,'RAND') && NM.TrainParam.RAND.InnerFold == -1 )
SVM.GridParam = 1; optimstr = ''; menusel = [];
else
opti... |
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