sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d3e7297a1a77c77b12f38d59e0083f8d26586f52b5e40fcd21b39087c7b6903b | MATLAB | 2,728 | 61 | %% Mutual Information Demo 3
% This demo goes through calculating the mutual information for two
% continuous data streams. This example demonstrates the use of predefined
% null models.
% Data Type: Continuous
% Number of Variables: 3
% Information Analysis: Mutual Information
% Trial Based or Single Trial: Single Tr... |
7484727010c888aa1d15e66526f90018bfb2c12e85c3ed9e4604a62f3bc0f29b | MATLAB | 2,729 | 72 | %% PaCER/EXAMPLE_1_1.m - Example file for using PaCER - Precise and Convenient Electrode Reconstruction
% to reconstruct precise curved electrode trajectories
% and contact locations from post operative CT imaging
% of DBS electrodes
%
% Andreas Husch
% ... |
c3d08e31ff6668eb043a9a973183c82303e5f63772455e67da47090e64db793d | MATLAB | 2,729 | 73 | function CBIG_ASDf_visualizeFactors(inputDir, outputDir, k, scalelim)
% CBIG_ASDf_visualizeFactors(inputDir, outputDir, k, scalelim)
%
% Function to compute factor-specific RSFC patterns and visualize the
% factors for K = 2 and 3.
%
% Input:
% - inputDir:
% Absolute path to the directory where factor est... |
b453a3ecee57276a68ed02d66fe065f343f047e6bb44b69cfcda4ab728821f12 | MATLAB | 2,730 | 103 | classdef ea_symmat < handle
% symmetric matrix object
% A. Horn
properties (GetAccess='private', SetAccess='private')
halfmat=[]; % stored half matrix
end
properties (SetObservable)
size % size of the original matrix
end
methods
function obj=ea_symmat(inmat) % generator function
... |
f3f066c2794e70188ac14583d36e036331642422b135e79f47cfc81459a2ff32 | MATLAB | 2,730 | 96 | function n = palm_effectiven(nP,EE,ISE,islog)
% Given a number of shufflings, compute the effective
% sample size.
%
% Usage:
% n = palm_effectiven(nP,EE,ISE,islog)
%
% Inputs:
% - nP : Number of shufflings (permutations, sign-flippings
% or permutations with sign-flippings).
% - EE : Boolean indicati... |
7a7f883a378ca69532bc2ffc222e014342924a8d9e3eade386ec626c79259419 | MATLAB | 2,731 | 110 | % Example 6.6: Comparison of worst-case robust, Tikhonov, and nominal least squares
% Section 6.4.2, Figure 6.16
% Boyd & Vandenberghe "Convex Optimization"
% Original by Lieven Vandenberghe
% Adapted for CVX Argyris Zymnis - 11/27/05
% (a figure is generated)
%
% Consider the least-squares problem:
% minimize ||... |
247d60978726a8269db57c4bf25fae49732bfc06289ade94c66c972fd352ca07 | MATLAB | 2,732 | 67 | function dir_angles = ea_diode_lightmarker(roll,pitch,yaw,marker)
vizz = 0;
%% create vectors symbolizing the gaps between directional contacts at 60, 270 and 300 degrees
% and transform them to match lead trajectory and directional level
marker = marker(1:3);
ven = [0 0.65 -0.75 ]';
dor = [0 0.65 0.75 ]';
[M,~,~,~] ... |
eafe980d5568ee8e70c8d087f2e883c8ed8aae4b4bbf699c747ed5b54e1407ff | MATLAB | 2,734 | 145 | function trainmodel
%%
%scheme = evalin('base','scheme');
d1 = 0.5+(0:0.05:1)*2.5;
d2 = 0+(0:0.05:1)*3;
d3 = 0.15+(0:0.05:1)*2.5;
v = 0:0.05:1;
[D1 D2 D3 V] = ndgrid(d1,d2,d3,v);
nt = 10^6;
D1 = 0.5+rand(nt,1)*2.5;
D2 = 0+rand(nt,1)*3;
D3 = 0.25+rand(nt,1)*1.5;
V = rand(nt,1);
%idx = find(abs(D1-(D2+3*D3))<1.5);
idx =... |
0b9b7bf3dc3d5afff8837db46366202c7bfb870e024955e0e1546e0df6d05ece | MATLAB | 2,737 | 70 | function ea_firstrun(handles,options)
% check if a newer version is available..
local=ea_getvsn('local',1);
web=ea_getvsn('web',1);
vcheck=0;
if strcmp(local,'Unknown')
vcheck=1;
elseif ~strcmp(web,'Unknown')
vcheck=(local<web);
end
try
if vcheck
set(handles.updatebutn,'Visible','on');
set... |
13be7ad1cafa1986db12e68ca757eef5b78eb6bf3a9f4d0da9196d3ba69a794c | MATLAB | 2,737 | 74 | function [fulltrial,types] = CEM_concat_analysis(thedata,frames)
% This is a function form of the script I run to get my concatenated
% dF/F data, specifically to process columnar data.
% First, navigate to the folder containing the folders of data you want to
% concatenate.
% example t... |
0334f6d307e580d4a96d98c85061171baf73f7ebd75a33c70a837c4d25b53d18 | MATLAB | 2,739 | 87 | function test_validity_of_datasource(ds)
% A helper function that tests whether a given data source returns any of the same data
% in the training and test data. Obviously if some of the same data is in the training
% and test sets then there are major problems with the datasource!
%
% The input of this function s... |
c84507b5871759ddf5701555fdb6c84f141dddb0a03281fd1f3b1f673218b14b | MATLAB | 2,739 | 69 | function [R, scale]=arqr(v, p, mcor)
%ARQR QR factorization for least squares estimation of AR model.
%
% [R, SCALE]=ARQR(v,p,mcor) computes the QR factorization needed in
% the least squares estimation of parameters of an AR(p) model. If
% the input flag mcor equals one, a vector of intercept terms is
% being fitt... |
96bfe73023c41476e228d2e0e05102253d1ed1582593f23ac90f946b1d92bdb2 | MATLAB | 2,740 | 33 | function [matlabbatch]=CalculateVDM(b)
%-----------------------------------------------------------------------
% Job saved on 15-Jan-2022 16:17:57 by cfg_util (rev $Rev: 7345 $)
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch... |
e8cd49c431167ba725fda3b58e666883675e094ac5644a4b2debe9523734c169 | MATLAB | 2,742 | 69 | %%
% This demo creates an artificial HRTF set.
% It shows how to use SOFAgetConventions and SOFAsave
% The HRTF set contains single pulses placed at sample index of 100
% which results in a broadband delay of 100 samples.
% Each IR is 256 samples long (i.e., N=256)
% SOFA API - demo script
% Copyright (C) 201... |
26843c7fd507488129aecfcf577640cf9ddf0ad9d196334e0dafcfcf3c2a0db8 | MATLAB | 2,743 | 61 | function flags = CBIG_MMLDA_check_example_results(out_dir)
%
% This function compares the example results saved in <out_dir> with the
% reference results.
%
% Input:
% - out_dir:
% The output directory where example results are saved.
%
% Output:
% - flags:
% flags is logical 5x1 vector that indicat... |
d386e2fea2652e36554107bdf9b61de002ea9b0a39e5ce2933e34da3a06b974a | MATLAB | 2,743 | 113 | %%**********************************************************
%% SDPT3soln_SEDUMIsoln: convert SQLP solution in SDPT3 format to
%% SeDuMi format
%%
%% [xx,yy,zz] = SDPT3soln_SEDUMIsoln(blk,X,y,Z,perm);
%%
%% usage: load SEDUMI_data_file (containing say, A,b,c,K)
%% [blk,At,C,b,perm] = read_s... |
243d0b11e6cc466866544f0dc62e0950a5c1eb45f93e8f1bbc8cd3edd416fa7f | MATLAB | 2,744 | 90 | function h = nifti(varargin)
% Create a NIFTI-1 object
%__________________________________________________________________________
% Copyright (C) 2005-2012 Wellcome Trust Centre for Neuroimaging
%
% $Id: nifti.m 4986 2012-10-05 17:35:09Z guillaume $
switch nargin
case 0
hdr = empty_hdr;
h = struct('hdr',h... |
64199eb11a7f5fb8b6104b3b995f2859be52615b1c52a6f06dbded1bc3ad75ec | MATLAB | 2,744 | 78 | %% Left Turns
% TO DO THIS, YOU NEED TO RUN THE CONTENT OF COMPUTETURNBOUTS2.M
Lturns = {}; leftPB = []; rightPB = []; turnLdata = []; PBcols = [];
Ltrials = []; Lflies = [];
count = 1;
for k = [1,2] % for these trial types
A = allflies([allflies.trtype]==k);
for n = 1:length(A)
for i = 1:leng... |
970c7595d2833a0e4e3ab62e9e95a26e12c29d2c57eb02550da06877f62dfe9e | MATLAB | 2,746 | 95 | function palm_hemimerge(varargin)
% Merge data for lh and rh (left and right hemispheres) into a
% single file. Various input files can be given, starting with
% 'lh' and/or 'rh'. The script finds the correct pair, removes
% repeated files, and merges them into files beginning with 'bh'.
%
% palm_hemimerge <files>
%
% ... |
2c4c8c00594d8bdf5f177a9d3c95ceea048a13da6647cb07c85a09f884960ae4 | MATLAB | 2,747 | 85 | % quantile() - computes the quantiles of the data sample from a distribution X
%
% Description:
% If F is the cumulative distribution function (CDF) of X,
% the p-th-quantile Qp of distribution X is the value for which holds
% F(x) < p, for x < Qp, and
% F(x) >... |
7360b1cb8b99926e740d1c2a3a061d2d788b62b630e7f473766fdc2d27eb47cc | MATLAB | 2,747 | 52 | function outinfo = cifti_diminfo_dense_get_volume_all_info(diminfo, cropped)
%function outinfo = cifti_diminfo_dense_get_volume_all_info(diminfo, cropped)
% Get information on how to map cifti indices to voxels.
% The volsform1 field is adjusted so that 1-based voxel indices (as returned
% in voxl... |
e3782ca8b8eefbb54947f8fbd4b0aef7ab441f7ffe5feda9400db743a83e7071 | MATLAB | 2,747 | 77 | function selected = SelectSpikes(spikes,varargin)
%SelectSpikes - Discriminate bursts vs single spikes.
%
% USAGE
%
% selected = SelectSpikes(spikes,<options>)
%
% spikes spike times
% <options> optional list of property-value pairs (see table below)
%
% ======================================... |
d1a3170e674c4a08c15593a15ad7c005761008f15ef122098094d7ac6d650a52 | MATLAB | 2,748 | 54 | % Get the visual connectivity for each condition
%[featureLabels,selectFeatureMat,conditionFeature,conditionFeatureMat,featureLabelIndex] = getFeatureLabel('C:\Users\yh19218\MATLAB Drive\PG\2_Codes\2019 Autumn\Task 1_Measure Classification\Alpha(LOO)',0.5);
map = imread('Empty.tiff');
load('channelPositions.mat')
c... |
4aedd1147c950e4e4af75954caf564ecdf4eb2275a97eb19c084587953f871a3 | MATLAB | 2,749 | 80 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
6839aa956d8e8a9d00bf49428d0a90297787c641746bccd00f0672ee3617bd8f | MATLAB | 2,749 | 61 | classdef CBIG_MMLDA_unit_test < matlab.unittest.TestCase
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
methods (Test)
function test_example(testCase)
CBIG_CODE_DIR = getenv('CBIG_CODE_DIR');
load(fullfile(CBIG_CODE_DIR... |
9d688bfbedadfc8ea9611edd91955bd3e9cb6d1cddd136edf5c53aba4298edf8 | MATLAB | 2,749 | 69 | function Obj=SOFAconvertSCUT2SOFA(root,r)
% OBJ=SOFAconvertSCUT2SOFA(root,pinna) loads the SCUT HRTFs saved in a
% directory ROOT for the radius R and converts to a SOFA object.
% R must be in meters.
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences;
% Licensed under the EUP... |
344208954b8a0a0f991dd8d340ecda36afe9122db42ad5476b1895aa6c5970fd | MATLAB | 2,751 | 67 | function [waveformDuration_peakTrough, peakLoc_forDuration, troughLoc_forDuration] = ...
computeWaveformDuration_peakTrough(thisWaveform, peakLocs, troughLocs, PKS, TRS, ephys_sample_rate)
% COMPUTEWAVEFORMDURATION_PEAKTROUGH Compute waveform duration from peak to trough
% This function implements the sophisticated... |
070bef992268a89bc7bab532bad626505ab4de28ffcbb1444a9f143ce85dca87 | MATLAB | 2,752 | 77 | function pvals = palm_datapval(G,Gvals,rev)
% Compute the p-values for a set of statistics G, taking
% as reference a set of observed values for G, from which
% the empirical cumulative distribution function (cdf) is
% generated, or using a custom cdf.
%
% Usage:
% pvals = palm_datapval(G,Gvals,rev)
%
% Inputs:
% G ... |
1b060af628eceb55254b5b78a790ea663cf089a022e616629dfa10341c201022 | MATLAB | 2,752 | 71 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
9a291a94f7d8ef5208639ca2a98310c64acdf10a191eca1d9df2424917886208 | MATLAB | 2,752 | 85 | function data = AFOFdata_struct_CL_3(inputdata, filenames)
% USE THIS FOR EXP9 (CEM)
% how it works:
% fly = AFOFdata_struct_CL_3(data,filenames) where data and filenames are
% outputs from AF_OF_importer()
for e = 1:length(inputdata)
for t = 1:size(inputdata{e}{1},1)
trial.filename = filenames{e};... |
425fbf9937d0f7533c28a55c2d1da44b0b85b545d61833dbb1acae17a25cdf63 | MATLAB | 2,754 | 76 | function [confRadTmp,centerTmp] = estimConfRad(tracks,probDim,confRadMin)
%ESTIMCONFRAD estimate confinement radius of tracklets
%
%INPUT: tracks (.tracksCoordAmpCG)
% Matrix indicating the positions and amplitudes
% of the tracked features to be plotted. Numb... |
c063568c0a17d0ebd5a6d80d76e0c0860d1242ca3ed21436436d45dde3e9cf3e | MATLAB | 2,754 | 76 | function trainModel(params, split)
% trainModel(params)
%
% ----------------------------------------------------------------------
% Matlab tools for "Predicting human gaze beyond pixels," Journal of Vision, 2014
% Juan Xu, Ming Jiang, Shuo Wang, Mohan Kankanhalli, Qi Zhao
%
% Copyright (c) 2014 NUS VIP - Visual Inform... |
f8efb0276385255dd9b6c8d9ad28f88e5e9729f045965aec40568aa77c8ad039 | MATLAB | 2,755 | 112 | xBF = spm_get_bf(struct('dt', 1, 'name', 'hrf (with time and dispersion derivatives)'));
% A canonical response
hrf = xBF.bf * [1 0 0]'; %[.6 -.6 -1]';
create_figure('hrf');
plot(hrf, 'ko:', 'MarkerSize', 6, 'MarkerFaceColor', [.4 .4 .4], 'LineWidth', 2);
set(gca, 'YColor', 'w', 'FontSize', 18);
xlabel('Time');
%% ... |
1408586987383c0e911e806d3582a1d884479377b273f6bfef1a1a2492442e70 | MATLAB | 2,756 | 86 | function mov=videoread(fname,varargin)
%VIDEOREAD Read an video file in a mannter compatible with Matlab's
% built-in AVIREAD function, but using a videoReader object to do
% the work instead.
%
% MOV=VIDEOREAD(FNAME)
% Read the video file FNAME into the Matlab movie structure MOV. MOV
% h... |
5256ae6a003947b812b8479963f232183b63bda477a1352aee72a7b245faf8ce | MATLAB | 2,756 | 85 | function ea_mod_tex(fname,options)
if exist([fname,'.aux'], 'file')
delete([fname,'.aux']);
end
if exist([fname,'.tex'], 'file')
delete([fname,'.tex']);
end
fID=fopen([fname,'.tex'],'w');
[pth,fn,ext]=fileparts(fname);
[~,patientname]=fileparts(pth);
% document header:
fprintf(fID,'%s\n','\documentclass{a... |
8487bdcb8b6a66fd6fab8dc93b9e4211c3d4342133e81c5c158bb9941df9dec8 | MATLAB | 2,756 | 69 | function obj=stat_density(obj,varargin)
% geom_point Displays an smooth density estimate of the data in x
%
% Example syntax (default arguments): gramm_object.stat_density('function','pdf','kernel','normal','npoints',100)
% the 'function','kernel', and 'bandwidth' arguments are the
% ones used by the underlying matlab ... |
9d6e5879c7bb0a96be929af85ff69817490e08ad7f7b7d8522f7b0ee7db9543b | MATLAB | 2,757 | 72 | %% PaCER/EXAMPLE_1_1.m - Example file for using PaCER - Precise and Convenient Electrode Reconstruction
% to reconstruct precise curved electrode trajectories
% and contact locations from post operative CT imaging
% of DBS electrodes
%
% Andreas Husch
% ... |
a62e120bf42272c7c2adf8f620d945a53a88a730f16343454c84ba4c94ef7480 | MATLAB | 2,757 | 107 | function [X, Y, Z] = domain2meshgrid(domain, resolution)
%DOMAIN2MESHGRID(domain, resolution) generate meshgrid on parallelepiped
% [X, Y] = DOMAIN2MESHGRID(domain, resolution) creates the matrices
% X, Y definining a meshgrid covering the 2D rectangular domain
% domain = [xmin, xmax, ymin, ymax] with resol... |
b00d11a4009268b70c134cdf55c390e28215db9c253cd9dc88c00be80f54763e | MATLAB | 2,759 | 72 | function run_tests(varargin)
%RUN_TESTS Headless entry point for the NONAN MATLAB test suite.
%
% From a shell, at the repository root:
% matlab -batch "addpath('tests/matlab'); run_tests"
%
% Optional name filter (substring match on test name):
% matlab -batch "addpath('tests/matlab'); run_tests('Surr'... |
b867e0538c7da5c6f33d0803595ed7fa2b2b7c1890a8992bfcd2b31eed13343b | MATLAB | 2,759 | 88 | function ea_warp_vat(b0rest, options, handles)
directory=[options.root,options.patientname,filesep];
if strcmp(b0rest,'rest') % processing rest files
b0rest=ea_stripext(options.prefs.rest);
end
stims=get(handles.vatseed,'String');
stim=stims{get(handles.vatseed,'Value')};
% check which vat-files are present:
vat... |
1bae0763a732473839bbe034ad5900230eeb1525e4ee842eda0b54b1575b5d6b | MATLAB | 2,761 | 80 | function saveNEVTetrodes(NEVFullFilename)
% saveNEVTetrodes
%
% Opens saves a new NEV file and splits it into smaller NEV files
% containing only the tetrodes according to the associated CCF file. The
% CCF file should have the same name as the data file.
%
% NEVFullFilename: The full path to the NEV to be opened.
%... |
bf469df91d3b83d617a0210d264510c35e76c0c0b9ee2a489c06c7d9aadff3e9 | MATLAB | 2,764 | 55 | % Session data handling functions for FMAToolbox.
%
% FMAToolbox provides a number of functions to handle data files stored
% in the open and hardware-independent <a href="http://neuroscope.sourceforge.net/UserManual/data-files.html">formats</a> used by <a href="http://klusters.sourceforge.net">Klusters</a>, <a href="h... |
ff44dc1fa1d62a002fb1f68987b1d642556302b59d51e04d85a9fd94bae18d62 | MATLAB | 2,765 | 101 | function y=calcRadius8(im,inv_flag,thr,imselect)
% Usage ... y=calcRadius(im,inv_flag,thr,imselect)
%
% This function measures the vessel diameter (in pixels) of im which
% is the image only including the vessel to measure
% thr(1) is the normalized projection threshold (default=0.5)
% additinal arguments include thr(2... |
6ab14b8b9a61775696ac608b08e2f6ac91249d7022ba583004c23180784c30a4 | MATLAB | 2,766 | 73 | function [all_erp_all_midi] = Trinh_MiniTrialMakerAmpEnv(data,note_onsets,code_corresponding_to_midi,n_offsets)
%
% midi_names = cell with strings containing the names of the files of
% interest
% code_corresponding_to_midi = trigger codes, present in the FieldTrip
% data structure, associated to the midi_names (N... |
49c7597d95083b452e8da0be78e1e8ba2e5e12e2479347a3277b81dbbc616caf | MATLAB | 2,768 | 93 | function [lab,q] = psdeig(x,K)
% [lab,q] = psdeig(x,K)
%
% PSDEIG Computes spectral coefficients of x w.r.t. K
% Arguments "q" is optional - without it's considerably faster.
% FLOPS indication: 1.3 nk^3 versus 9.0 nk^3 for nk=500,
% 1.5 nk^3 9.8 nk^3 for nk=50.
%
% ********** INTERNAL ... |
869e77820276e9a08772e0cbebf121931f0a33a84035fd822171d7e06c34b790 | MATLAB | 2,770 | 70 | function nice
%NICE Custom plot prettification.
% The function NICE is a macro for Matlab graphics settings, and its
% behavior depends on the contents of the current axes.
%
% If the plot contains only 2-D objects (i.e., objects with empty ZData)
% NICE sets the Y-limits depending on the data:
% ... |
f5358a7bef34320972ed7f94d51ed673b98af85dba0f8e59e319d97bb46b6148 | MATLAB | 2,770 | 89 | function derivative = Diff(samples,varargin)
%Diff - Differentiate.
%
% USAGE
%
% derivative = Diff(samples,<options>)
%
% samples data to differentiate
% measured in number of samples (default = no smoothing)
% <options> optional list of property-value pairs (see table below)
%... |
daca56f9af4998c5ea08760765976a5e935aec205cf975b2bca5562a950c0f1c | MATLAB | 2,774 | 79 | function epochs = SelectEpochs(epochs, validepochs, partials)
% Takes epochs that exist within valid epochs,
% CMBHOME.Utils.SelectEpochs(epochs, validepochs)
%
%
% INPUTS
% epochs - Nx2 array, epochs (time1 time2;...)
% validepochs - Mx2 array, epochs
% partials - (default 1) logical, 1==return pa... |
ffa1ef0c470be600ee30e65d871f2ba1d7dbb2202fbc01ebc1496755eb34bb56 | MATLAB | 2,775 | 79 | function [res, errStr, verStr]= ftrstruct_istype(dataIn, fiberType)
%function [res, errStr]= ftrstruct_istype(dataIn, fiberType)
%
% function determines if dataIn is a valid ftrStruct or fiberStruct. If this is the case,
% also the type name is returned as the second return value.
%
% Type Explanation:
% ftrS... |
bc2026678632d9790862f83dc8ec321d6916b077a7a18b7f51fd899115266a93 | MATLAB | 2,777 | 73 | function [AllX,space]=ea_exportefieldmapping(vatlist,obj)
EFthresh = 50;
templateresolution = .5;
if size(vatlist,2)>1
sidesuffices={'_r','_l'};
else
sidesuffices={''};
end
disp('Need to export Efields in proper format, this may take a while');
outdir=[fileparts(obj.leadgroup),filesep,'sweetspots',filesep,obj.I... |
389cf23742cbb19844efeba372a0fecfa78517078355628953bcc6c934fa7024 | MATLAB | 2,778 | 111 | function [n, nm, nl, ts, names, m] = nex_marker(filename, varname)
% nex_marker(filename, varname): Read a marker variable from a .nex file
%
% [n, nm, nl, ts, names, m] = nex_marker(filename, varname)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% varname - variable name
%
% continu... |
4daaa34dd99e2baa2a2197ab95f7664e5050310eb6000be34a496af05627216e | MATLAB | 2,779 | 58 | % SOFA API - script demonstrating the usage of variables in the API
% Copyright (C) 2012-2013 Acoustics Research Institute - Austrian Academy of Sciences
% Licensed under the EUPL, Version 1.1 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "License")
% You may no... |
3edd8ee35ab6b8af43fbf2146fd6114c72aeab017cd2740a0f3b5909a3e48269 | MATLAB | 2,780 | 52 | function isargchar(varargin)
%ISARGCHAR tests if the given arg is a char and returns an error otherwise
%
% Usage: isargstruct(arg1,arg2,...)
%
% Input options:
% args - list of args
%
% ISARGCHAR(args) tests if all given args are a char and returns
% an error otherwise.
%
% see also: ... |
0dc69709d66d5fce274847089cdb8fe897fecf7d5d568005c559dc3045151726 | MATLAB | 2,782 | 94 | function [im,info]=readOIS3(fname,imno,prec,do_write)
% Usage ... [im,info]=readOIS3(fname,imno,prec,do_write)
% prec=[1:uint8,2:uint16,4:single,8:double];
if nargin<4, do_write=0; end;
if isempty(do_write), do_write=0; end;
do_transp=1;
if strcmp(fname(end-2:end),'raw'),
if nargin==1, imno=1; end;
... |
7f095bc1a373c889fe436f1040142df153d6cd20a60ab187ecc4e9f9274f4b7e | MATLAB | 2,782 | 102 | function [ent_samp_value] = ent_samp(data, m, r, flag)
%SAMPEN Calculate the sample entropy of a time series.
%
% ent_samp_value = ent_samp(data, m, r, flag)
%
% Inputs:
% data - A vector containing the time series data.
% m - Embedding dimension.
% r - Tolerance threshold. If flag is 'prop'... |
712b8e190b18f44e2887c2eb487e57e4085d2038fd43c11fe8c292e146f9eb8a | MATLAB | 2,783 | 78 | % useage:
% printFigs(figNums, folderName)
% printFigs(figNums, folderName, format)
% printFigs(figNums, folderName, format, fileTitles)
%
% figNums is just a list of the figure numbers (e.g., 1:10)
% if folderName doesn't exist, it will be created, and you will be told
%
% fileTitles is a cell array of str... |
15647287602077c6d61df19aeaf74e56a14f82e0684f581cffeee518ace0e5d9 | MATLAB | 2,784 | 101 | function [d, ax] = gridDistance(self,Pd,thresh,fromCenter,ifplot)
% Calculates and returns the distance from the center Acorr peak to the
%
% Inputs: self -- CMBObject, function assumes self.cel is set
% Pd -- "PeakDistance", the minimum distance between peaks.
% Defaults to 7, which works for most ce... |
3b4c6f5f0ec569346ceb8724dd943c3a27f4aedb6d057a0a66e1a6ff9c8b1094 | MATLAB | 2,784 | 101 | %% figure S4
% Consistency of wave motifs across individual sessions.
% (A) Awake state: session-level motif frequency with chance level
% (B) Anesthetized state: same as (A)
load('figureS4_data')
%% Parameters
n_time = 300;
chance_val = n_sessions / n_clus; % 45/7 ~ 6.43
% Colors: gem palette
motif_colors = ... |
de05e4bb7ccee850f015bfce14ff1142241a35f7447d439caf517bc6a66ff839 | MATLAB | 2,784 | 70 | function analyzeCalciumExperiment_newThor(headpath,fileexpnum,imskip,expskip,correction,fluor,copy,savemode)
%give this function the experimental path you want to start in
%and the filename and experiment number (ie vt019532_f3e4)
%correction if the motion correction needs to be done, fluor if the dff
%hasn't been extr... |
09590bb00e4832560fe87183f263389f6dd526c9ec0b3287464cd0405d44e979 | MATLAB | 2,788 | 91 | %% Add all folders to path
addpath(genpath(pwd));
%% Load raw data
data = data_WT_raw();
k = 1000; % scaling factor
alpha = 0.01; % filtering parameter
%% Process all NSC counts and fractions
proc = process_NSC_frac_data(data, k, alpha);
%% Define scenarios for comparison
scenar... |
2d1208c2bd65f612751e16b57cf07ccdfd98aeca3595f5fbfcfba1e5faaeeec4 | MATLAB | 2,788 | 89 | %%******************************************************************
%% randlowranksdp.m : creates random feasible SDP problems where the
%% constraint matrices are low-rank matrices of the
%% form V*diag(d)*V'.
%%
%% [blk2,At2,C,b,blk,At] = randlowranksdp(n,m1,m2,r);
%%
%% blk2,... |
7421e8c647eafd247040b1b86c84c6cd31c5f9546460d7aa318930eff20fa8e0 | MATLAB | 2,789 | 97 | % posact() - Make runica() activations all RMS-positive.
% Adjust weights and inverse weight matrix accordingly.
%
% Usage: >> [actout,winvout,weightsout] = posact(data,weights,sphere)
%
% Inputs:
% data = runica() input data
% weights = runica() weights
% sphere = runica() sphere {... |
f80fb55210c583415fb4aa3852251a702baf495334b6db5a4b95d1086292ef6c | MATLAB | 2,789 | 124 | function y = log_sum_exp( x, dim )
%LOG_SUM_EXP CVX internal version.
narginchk(1,2);
cvx_expert_check( 'log_sum_exp', x );
sx = size( x );
if nargin < 2 || isempty( dim ),
dim = cvx_default_dimension( sx );
elseif ~cvx_check_dimension( dim, true ),
error( 'Second argument must be a valid dimens... |
2f75938e299bb5781d290ff0dc1e978db99fff199792527aabcc7d8117af91d2 | MATLAB | 2,790 | 55 | % Contact ythomas@csail.mit.edu or msabuncu@csail.mit.edu for bugs or questions
%
%=========================================================================
%
% Copyright (c) 2008 Thomas Yeo and Mert Sabuncu
% All rights reserved.
%
%Redistribution and use in source and binary forms, with or without
%modification, a... |
3323a59c1e37a0204d839bd571161a5855b899a481324c64e876b729a1476917 | MATLAB | 2,790 | 65 | %% Transfer Entropy Demo 1
% This demo goes through calculating the transfer entropy between 2
% continuous time series with time locked trials.
% Data Type: Continuous
% Number of Variables: 2
% Information Analysis: Transfer Entropy
% Trial Based or Single Trial: Trial Based
% Significance Testing: On
% Delays: Off
... |
380a5f3a11507388a48ab5705ac1f595b8962e08aee0c6868bff513ddc2bcc46 | MATLAB | 2,790 | 52 | function isargstruct(varargin)
%ISARGSTRUCT tests if the given arg is a struct and returns an error otherwise
%
% Usage: isargstruct(arg1,arg2,...)
%
% Input options:
% args - list of args
%
% ISARGSTRUCT(args) tests if all given args are a struct and returns
% an error otherwise.
%
% ... |
a9b251236cfe9444da32912ff80c9161ec7b429250484834ff5f132e3770c2a4 | MATLAB | 2,792 | 111 | function [V,t,Err] = evoked(data,Fs,win,width,plt,err)
% Function to calculate the evoked response given continuous data in the
% form time x channels
% Usage [V,t,Err] = evoked(data,Fs,win,width,plt,err)
%
% Inputs
% Note that all times can be in arbitrary units. But the units have to be
% consistent. So, if wi... |
9ddb1479b658a553d5f50012015c83531cbcea4c8975396bbe9baa77283dd55e | MATLAB | 2,793 | 108 | function y = cumprod( x, dim )
% Disciplined geometric programming information for PROD:
% CUMPROD(X,DIM) is a vectorized version of multiplication,
% so in most cases it would be incompatible with DCPs. Therefore it
% has not been implemented to support DCPs. DGPs however support
% product... |
6e7ee5b1e0cddd0dbe825aa9a3c0fc33b71093edf39b1dd8839df9606a1d8846 | MATLAB | 2,794 | 87 | %% Example 2 of applying author topic model (AT)
%
% This example shows how to run the AT Gibbs sampler and extract samples
% from the same and different chains.
load 'bagofwords_nips'; % load the nips word document dataset
load 'authordoc_nips'; % load the author-document pairings for nips
load 'words_nips'; ... |
7d3e63c714d59f723e385a3a350219e3b65e72209f20f43fc53798452569fdf3 | MATLAB | 2,794 | 115 | function [HIPshank, ECshank]=getshankECHIP_LV(animal)
if strcmp(animal, '3xTg1-1')==1
HIPshank=3;%2
ECshank=5; %5
elseif strcmp(animal, '3xTg1-2')==1
HIPshank=4;%3
ECshank=6;
elseif strcmp(animal, 'WT45-2') == 1
HIPshank =3;
ECshank =5;
elseif strcmp(animal, 'AD-WT-1-0') == 1
... |
a9baafc49a6455090fab34a1353ed97e1b0cdaf0931b803b2ab8ba82e06a82bf | MATLAB | 2,795 | 122 | function out = HTML(in,format)
%HTML - Create HTML formatted string.
%
% Important note: Matlab UITables are buggy! Therefore, HTML formatted table
% cells will not be rendered satisfactorily (e.g. you will experience problems
% with alignment and cell width). This function does not try to compensate for
% these b... |
7bebe138185ed87d726a20c17ca443ba640cb3bd590d00bf6371338e70db2fde | MATLAB | 2,797 | 72 | function [r] = ea_circcorr(y,X,exponent)
[~,score] = pca(X);
if ~exist('exponent','var')
exponent=1.5;
end
res=ea_nanzscore(ea_resid(score(:,1:5),y));
weights=abs(res).^exponent;
cnt=1; chunks=40; % a chunk of 40 seems to be a good speed tradeoff for this operation.
%ea_dispercent(0,'Iterating voxels');
nsz=siz... |
b1d4f0cfa665ae5fde14ae1d323df882e30b43f6375c143d67bfbf9976f90eea | MATLAB | 2,797 | 83 | function CBIG_IndCBM_cifti2nifti(cifti_file, mask_file, output_file, colortable)
% CBIG_IndCBM_cifti2nifti(cifti_file, mask_file, output_file, colortable)
%
% This function write cerebellar parcellation/confidence in cifti file into
% a nifti file.
%
% Input:
% - cifti_file:
% Path of the cifti file ne... |
a3ce9ea7c82950ac88c24a8bc250a56ef00e08b1b4553781361db9dcc3d8e173 | MATLAB | 2,798 | 57 | function avgCorr = CBIG_ASDf_indivCorr2avgCorr(lh2lh_corr, lh2rh_corr, ...
rh2rh_corr, lh2subcor_corr, rh2subcor_corr, subcor2subcor_corr)
% avgCorr = CBIG_ASDf_indivCorr2avgCorr(lh2lh_corr, lh2rh_corr,
% rh2rh_corr, lh2subcor_corr, rh2subcor_corr, subcor2subcor_corr)
%
% This function averages hemispheric/subcortica... |
0c1d5d5ed193709d282d29e9b44e7ebd322d38883ac526ff1e13942e85766f71 | MATLAB | 2,799 | 105 | function [zeitgeberTime relativeTime absTime] = bz_getZeitgeberTime(basename,downSampleFactor,samplingRate)
% assumes pwd is basepath for now
%% get timestamps for recording starts
parts = strsplit(basename, '_');
date = parts{end-1};
if strcmp(parts{end},'merge') % if multiple sessions are merged, find the start ti... |
388b7082b2428e04a16935c0abb25abbf50cdca04f4650b7adbf36c504065580 | MATLAB | 2,799 | 93 | function [p_shuf, r_dist] = shuf_test(map1, map2, varargin)
%
% Usage:
% [p_shuf, r_dist] = shuf_test(map1, map2, varargin)
%
% Description:
% Shuf permuation (author: @saratheriver)
%
% Inputs:
% map1 (double array) - One of two map to be correlated
% map2 (double array) - The other map to be correlated
%
% ... |
951afedfc98fc955947a08388bf513421780c8809a08f150719d1cbe8646d655 | MATLAB | 2,799 | 75 | function [up,down] = ZeroCrossings(data,varargin)
%ZeroCrossings - Test zero crossings in a given time series.
%
% This assumes a minimum of 10 samples per positive/negative phase.
%
% USAGE
%
% [up,down] = ZeroCrossings(samples,<options>)
%
% samples an Nx2 matrix of (timestamp,value) pairs
% <optio... |
e9899557af3f53915080eb8eecaabfd21403cc57f7e5c3d8570e28c53c78fb38 | MATLAB | 2,800 | 94 | function Par = LoadPar(FileName, varargin)
% % LoadPar(FileName)
% % loads the specified par file and returns a structure with these elements:
% %
% % .FileName -> name of file loaded from
% % .nChannels -> number of total channels
% % .nBits -> number of bits of the file
% % .SampleTime -> time, in... |
210ab4276746c4047f786fff0d08ffec168f227ff867482ef0643f70dc79500a | MATLAB | 2,802 | 81 | % pcsquash() - compress data using Principal Component Analysis (PCA)
% into a principal component subspace. To project back
% into the original channel space, use pcexpand()
%
% Usage:
% >> [eigenvectors,eigenvalues] = pcsquash(data,ncomps);
% >> [eigenvectors,eigenvalues,com... |
77240ebd291a9d04bfe03ae25c3368f9472451e95fb46c4eaf094880d79340bf | MATLAB | 2,802 | 73 | function varargout = getsamples(filename, varargin)
% Read samples from acq file
% filename - acq file
% varargin - channel names
% Returns column vectors of all channel data samples of requested channels.
% Example:
% [SourceR, EMG_L, EMG_R] = getsamples('myfile.acq', 'SourceR', 'EMG_L', 'EMG_R');
% Note:... |
840fb724493a915653e058ed8082954644185ccbd2471ef2314db90a572c6490 | MATLAB | 2,802 | 52 | function isargfile(varargin)
%ISARGFILE tests if the given arg is a file and returns an error otherwise
%
% Usage: isargfile(arg1,arg2,...)
%
% Input options:
% args - list of args
%
% ISARGFILE(args) tests if all given args are a file and returns
% an error otherwise.
%
% see also: is... |
c571f89f533b69cb0730f3b7effdaa7df06060cf99ab59c873a50eb779ed8744 | MATLAB | 2,802 | 82 | function [rev,file] = headRev(folders,strs,rec)
%HEADREV Retrieve the head revision for specified files
%
% This function finds the most recently committed file in the specified
% folders(s) and returns its revision and filename. The files must
% contain the 'Revision' and 'Date' keywords.
%
% REV = IOSR.SVN.... |
8943f7ecc57c9e45b4f2434307f69c30c4172af8e47da7165559edd2829bda16 | MATLAB | 2,803 | 116 | function [a, b] = isintent(this,intent)
% Correspondance between fieldnames and NIfTI intent codes
% FORMAT ind = isintent(this,intent)
% this - GIfTI object
% intent - fieldnames
% a - indices of found intent(s)
% b - indices of dataarrays of found intent(s)
%________________________________... |
58f125d2f2abaf7ce821271732ac7ab4e145d6bb580689c50d50d71e425551f0 | MATLAB | 2,804 | 60 | function ea_set_ANN_training(reco_file,stim_folder,minCylindricCurrent,maxCylindricCurrent,minSegmentedCurrent,maxSegmentedCurrent)
% Set ANN training parameters and prepare OSS StimSets (Should be moved to GUI)
% By Butenko, konstantinmgtu@gmail.com
arguments
reco_file % Lead-DBS options for ele... |
9f7a555bff5574939a0835813a42c63e928a6832ef27f2f468545b08759376a5 | MATLAB | 2,804 | 84 | function test_layouts
%%
msgid = 'matlab_bgl:test_layouts';
%% circle_graph_layout
X = circle_graph_layout(sparse(4,4));
Y = [1 0; 0 1; -1 0; 0 -1];
if norm(X-Y)>5e-6, error(msgid, 'circle_graph_layout(4) bad coords');
end
%% fruchterman_reingold_force_directed_layout
G = cycle_graph(10,struct('directed',0));
X = f... |
8ecd36766af8d0c492b0cfe6d7448be2a1035740efef33ca5a497c4b684a46c7 | MATLAB | 2,807 | 123 | function [xyz_minmax, dim] = axes_extremal_xyz(ax)
%AXES_EXTREMAL_XYZ Minimum and maximum coordinates of graphics objects.
%
% usage
% [xyz_minmax, dim] = AXES_EXTREMAL_XYZ(ax)
%
% input
% ax = axes object handle
%
% output
% xyz_minmax = coordinate extremals of objects in axes ax
% = [xm... |
964637525958bc5b46b119ab375cad3fceba59ccbef9eee90529d5a52927da7e | MATLAB | 2,808 | 91 | function tree = struct2xml(s,rootname)
% STRUCT2XML Convert a structure to an XML tree object
% FORMAT tree = struct2xml(s,rootname)
%
% Convert the structure S into an XML representation TREE (an XMLTree
% object) with ROOTNAME as the root tag, if provided. Only conventional
% objects (char, numeric) are accepted in S... |
ab6a511c0ba913f257e5e3327f7f87dcb7b6f8c9cf1b54bfe34eb5591db51057 | MATLAB | 2,808 | 68 | function ea_plot_prob_fiber_state(varargin)
% example
% ea_plot_prob_fiber_state('/media/konstantin/Konstantin/StimFit_Cohort/StimFitBIDS/derivatives/leaddbs/sub-SBN7F4E4/stimulations/native/gs_20230506011354/sub-SBN7F4E4_sim-fiberActivation_model-ossdbs_hemi-L_tract-cerebellothalamic_left.mat', 125)
fib... |
8b2914279fd1228d5724d9c61f17b2c114fd1b3448f0ba386923ce22ad34e2ff | MATLAB | 2,811 | 91 | function tree = struct2xml(s,rootname)
% STRUCT2XML Convert a structure to an XML tree object
% FORMAT tree = struct2xml(s,rootname)
%
% Convert the structure S into an XML representation TREE (an XMLTree
% object) with ROOTNAME as the root tag, if provided. Only conventional
% objects (char, numeric) are accepted in S... |
c77e6d3cfc1fec4ee0b5885e5cdd5c46c86ab1b5aaacd43787f62027e5f4d437 | MATLAB | 2,812 | 87 | function [x] = ft_struct2double(x, maxdepth)
% FT_STRUCT2DOUBLE converts all single precision numeric data in a structure
% into double precision. It will also convert plain matrices and
% cell-arrays.
%
% Use as
% x = ft_struct2double(x)
%
% Starting from MATLAB 7.0, you can use single precision data in your
% comp... |
1175a8a4824b8647651d686b66c43cc8c604bb2c944ed760b9032d886c9404db | MATLAB | 2,815 | 84 | %%*******************************************************************
%% detect_ublk: search for implied free variables in linear
%% block.
%% [blk2,At2,C2,ublkinfo] = detect_ublk(blk,At,C);
%%
%% i1,i2: indices corresponding to splitting of unrestricted varaibles
%% i3 : remaining indices in the linear ... |
4abea88e10989d6004867696b08fd1086e693e45c7d971f4463fa2b8f2192e81 | MATLAB | 2,815 | 63 | %Baseline
%load 'StimSM', stimAllTrials';
tstart_i=-2;
tstop_i=0;
% (StimCombined.m, stimAllTrials.mat)
rr1a_percentmeansBase=nanmean(all_rr1a_percent(tt>=tstart_i&tt<tstop_i,:));
rr1a_percentsemBase=nanstd(rr1a_percentmeansBase)/sqrt(size(rr1a_percentmeansBase,2));
yproj2max_percentmeansBase=nanmean(all_yproj2... |
3a6df272d3c7b5b8bba103f26011319b90eb2e521637f87c567ad120156e88a0 | MATLAB | 2,816 | 67 | function ea_get_field_from_csv(ref_image, Field_array_file, Activation_threshold_VTA, sideLabel, outputBasePath, source_index)
ea_dispt('Creating nifti header for export...');
% create nifti
[~, ~, endian] = computer;
switch endian
case 'L'
endian = 0;
case 'B'
endian = 1;
end
% split to corrd... |
827e8531f7b4bcafc8de4b030147fb76662a70703a2fab4c7ff7940c09b09727 | MATLAB | 2,816 | 87 | function data = AFOFdata_struct6(inputdata, filenames)
% USE THIS FOR EXP6 (CEM)
% how it works:
% fly = AFOFdata_struct6(data,filenames) where data and filenames are
% outputs from rotoball_importer()
for e = 1:length(inputdata)
for t = 1:size(inputdata{e}{1},1)
trial.filename = filenames{e};
... |
11c918ee2d2ebb9b9cb06cac9af4406a5b3c88a0e544183b6ce1a38975752b77 | MATLAB | 2,818 | 69 | function lscovalldat(alldat)
rhos={};
pvals={};
colours=colormap(hsv(numel(alldat)));
%colormap(gray(101));
f=figure; hold on;
for k=1:numel(alldat)
eightcols=linspace(1,8,numel(alldat{k}.mavgx));
x1=eightcols';%make to column format for lscov
y=alldat{k}.ang';
X=[ones(size(x1)) x1];
a=X\y;
... |
130d2459191a158087ed35587f6297517494e93f9bcfc44187041b82d8bfc816 | MATLAB | 2,818 | 93 | %% Fast Spiking Interneuron (FSI) Izhikevich Model Neuron
% Produces simulated data for a simple model of a fast spiking interneuron
% from Izhikevich 2007, page 299, Figure 8.27.
%
% Syntax: [mv,spkCt,spkLoc] = simpleModel_FSI(vInput,T,tau,PLOT,nzInput)
%
% Input:
% vInput (1 by number of time steps double vector) -... |
3a2a2a35c2eb2a2a4ba33dc3e6651b78730ed009176034d7f381d9151b28ac7c | MATLAB | 2,818 | 91 | function p = MultiPlotXY(varargin)
%MultiPlotXY - Plot two columns of each input matrix against each other.
%
% Plot the second column of each input matrix as a function of the first column.
% Optionally, alternative pairs of columns can be plotted against each other.
%
% USAGE
%
% p = MultiPlotXY(X,columns,Y,colu... |
8d6bfe2ea1320a9ec319a3961f8e01aaee8aae65b156fd80c6a9ca96b974bb07 | MATLAB | 2,818 | 88 | %%*******************************************************************
%% HKMpred: Compute (dX,dy,dZ) for the H..K..M direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*******************************************************************
func... |
b6f85238055bcbfa90015d81a260aae03663d58531c93a23f23d4ab00ea220d3 | MATLAB | 2,818 | 98 | %% Getting started: add paths
addpath(genpath('/Users/wani/github/canlabrepo/CanlabCore'));
%% Reading images (you don't need this part now)
% basedir = '/Volumes/engram/labdata/current/BMRK3';
% imgs = filenames(fullfile(basedir, 'Imaging/*/Models/Temp/beta_000[1-5].img'));
% mask = fullfile(basedir,'pain_2s_z_val_... |
0dcd72ee785381bfac232544e76564e49c72367c1af4a581950a23874aa5bbb1 | MATLAB | 2,819 | 115 | %% THIS IS an ad hoc script for organizing an existing set of fmri_data objects into
% a cell array in DATA_OBJ
dofullplot = 1;
DATA_OBJ = {};
DATA_OBJ = {ant_Baseline_HH ant_E heat_Baseline_HH heat_E};
n = length(DATA_OBJ);
for i = 1:n
DAT.imgs{i} = DATA_OBJ{i}.fullpath;
end
% add placeholder wildcards
fo... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.