sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3537739d8a8f1cb8cf6da1e50cc326d4fee736d6106ff5fbe9735f8ca609d84b | MATLAB | 1,220 | 65 | function epochs = MergeEpochs2(epochs, mergetouching)
% merge epochs of arbirary precision without creating binary vector
%
% epochs = CMBHOME.Utils.MergeEpochs2(epochs, mergetouching)
%
%
% returned sorted
%
% andrew 10/13/2011
% Updated: Ehren Newman, 19th November 2012. Sped-up.
OE = epochs;
if ~exist('mergetouchin... |
78f275a4c7e3badb36d203e50a106d511f603923dd2c482646592089727583e0 | MATLAB | 1,220 | 29 | %% plotIntensityProfileAndPeaks
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function plotIntensityProfileAndPeaks(intensityProfile, skelScaleMm)
filterIdxs = find(sk... |
7c95e69f8eb60fc63a143e70ba2f33353d7ec8b1966fb0bda28af886a39ccab0 | MATLAB | 1,220 | 36 | function halfWidth = calculateHalfWidth(spikeWidth)
% CALCULATEHALFWIDTH Calculate half-width for spike extraction
%
% This function calculates the appropriate half-width (samples before/after peak)
% based on the total spike width.
%
% Input:
% spikeWidth - Total number of samples in the spike waveform
%
% Output:
%... |
c4519f719ef37239e7d6b18235cfff6cf8d107fc9a2c92e33a15c39741b3ddc6 | MATLAB | 1,220 | 40 | function [D,P] = floyd_warshall_all_sp(A,varargin)
% FLOYD_WARSHALL_ALL_SP Compute the weighted all-pairs shortest path problem.
%
% The Floyd-Warshall algorithm for the all-pairs shortest path problem
% works only on graphs without negative edge weights. This method should
% be used over the Johnson algorithm for de... |
203e804696689bf0df1330ceb2d4f17d59dcda23889af4c3c2cd5af0091ded60 | MATLAB | 1,221 | 26 | function ea_add_discfiber(~,~,leadgroup,resultfig)
% small function to open ea_discfiberexplorer. lead group can be a path to
% either lead group analysis file or saved fiber explorer.
if ismember('M', who('-file',leadgroup)) % Add new discfiber analysis
exp = ea_discfiberexplorer(leadgroup,resultfig);
tractId... |
3f020dc72d065f0eb4be0b46722c6c1ad7655c3af9857b95b7e98cc432dae0fb | MATLAB | 1,221 | 26 | function a = gt( x, y )
%Disciplined convex programming information for GT (>):
% The right-hand side of a less-than constraint must be convex. The
% left-hand side must be concave. Of course, real constant and affine
% expressions are both convex and concave and can be used on either
% side as well.
%
%Discip... |
609de24c53d05b8c43b876d3eba23368454bc59cf2ca6ead8afac1d35cf7c909 | MATLAB | 1,221 | 44 | % Euclidean projection on the semidefinite cone
% Sec. 8.1.1, Boyd & Vandenberghe "Convex Optimization"
% Joelle Skaf - 10/07/05
%
% The projection of X0 on the proper cone K = S+^n is given by
% minimize ||X - X0||_F
% s.t. X >=0
% where X is a nxn matrix and ||.||_F is the Frobenius norm... |
4d2820253134c88e8567d8e690bff0a05779e14f566dcd810dabe0ab1ff9e809 | MATLAB | 1,222 | 36 | function padded = padmatrix(input, wherepad, padval)
%PADMATRIX Pad a matrix.
% PADDED = PADMATRIX(INPUT, WHEREPAD) adds zero rows/columns to the
% matrix INPUT. WHEREPAD is a four element vector specifying the number
% of pad rows/cols beyond [left col, right col, top row, bottom row].
%
% PADDED = PA... |
6694e08da1388ca804bd3415d0d08fcb36e46dc785068738b904713df04708e1 | MATLAB | 1,223 | 36 | function uid = root(tree)
% XMLTREE/ROOT Root Method
% FORMAT uid = root(tree)
%
% tree - XMLTree object
% uid - UID of the root element of tree
%__________________________________________________________________________
%
% Return the uid of the root element of the tree.
%_______________________________... |
d195ae5a123068cb2f7333e26dac1ac0a376fd5fa1224cb47400708ad7d39eb0 | MATLAB | 1,223 | 31 | function Y = CORE_leadingedges(X)
%CORE_LEADINGEDGES Core computational routine for LEADINGEDGES.
% Y = CORE_LEADINGEDGES(X) takes an M x N matrix X and returns a M x N
% matrix Y, containing a logical 1 in each location Y(j,k) such that
% X(j,k) AND ~X(j,k-1) for k>1 and X(j,k) for k==1.
%
% The matrix Y is of... |
e97fd0dbb643421857b600a24743a73564aa51ddec8454a8c99b7fbb0bcafff6 | MATLAB | 1,223 | 43 |
addpath bva-io-master/
addpath (genpath('eeglab2022.1/'));
eeglab
load("dataset_ds005284.mat");
folder = 'EvokedPotentialPlots';
htmlGray = [128 128 128]/255;
channelLabels = {data{1}.chanlocs.labels};
for figi=1:length(channelLabels)
gcf= figure();
hold on
averagedERP = zeros(size(data,2),1200);
for ... |
4e6d08e9d6802a421d6bf1f453fffdb9eafe5dcabd34636bfc932dac36004418 | MATLAB | 1,224 | 26 | function a = ge( x, y )
%Disciplined convex programming information for GE (>=):
% The right-hand side of a less-than constraint must be convex. The
% left-hand side must be concave. Of course, real constant and affine
% expressions are both convex and concave and can be used on either
% side as well.
%
%Disci... |
86e7fa1835614aab8b09b59aa1ee47e422ec69bda3fd18e34c57c6ea0a833612 | MATLAB | 1,224 | 58 | % This is a demonstratin of FRID framework using a simulated dataset
%% Clear all
clc;
clear;
close all;
%% Add path
addpath('./util/');
addpath('./FRID/');
%% Load data and pre-process
dataset_path = './Sim3_p0.1_mini.mat';
load(dataset_path);
[nN,nT]=size(Fr);
ns=length(unique(id_true)); % Number ... |
31f8cdef8330949b914385e4f9858513a88ed5d93dfe895f92623fdbe2eaa945 | MATLAB | 1,225 | 36 | function tree = delete(tree,uid)
% XMLTREE/DELETE Delete (delete a subtree given its UID)
%
% tree - XMLTree object
% uid - array of UID's of subtrees to be deleted
%__________________________________________________________________________
%
% Delete a subtree given its UID
% The tree parameter mus... |
44c147568fc03a75cda4c2b6e287e58ad4e98dbbe78a057be30fee194b9fc82d | MATLAB | 1,225 | 40 | function p = PlotXY(X,varargin)
%PlotXY - Plot two columns of a matrix against each other.
%
% Plot the second column of a matrix as a function of the first column.
% Optionally, alternative pairs of columns can be plotted against each other.
%
% USAGE
%
% p = PlotXY(X,columns,<options>)
%
% X the ... |
96939aaf652d64f3f2f8d85ec3c6f975ed49ca2b73ab2452edcddd8ebb8dc652 | MATLAB | 1,226 | 37 | function maxLV = capLV(maxLVopt, Xtrain)
% capLV Cap the number of PLS latent variables to what the data support.
%
% maxLV = capLV(maxLVopt, Xtrain)
%
% Returns the largest latent-variable count that is valid for this training
% fold: min(requested, rank(Xtrain)-1, nTrain-2), floored at 0.
%
% Inputs
% ma... |
b824f0ce8ce1561a5fcb5592f6adb7fd6101b229c6a4644797cc662b42251449 | MATLAB | 1,226 | 46 | function [A xy] = cycle_graph(n,varargin)
% CYCLE_GRAPH Generate the cycle graph of order n
%
% The cycle graph is a simple cycle with n vertices.
%
% [A xy] = cycle_graph(n) generates a cycle graph with n vertices and
% returns the adjacency matrix in A. The matrix xy stores two-dimensional
% coordinates for ... |
cbf4220e923757ab7e475a19d86e64ba03ba19f6547ae76b572924624f59543a | MATLAB | 1,226 | 35 | function varargout=ea_explorer_stats_meanmap(varargin)
% Function to estimate a certain mass univariate test (see below) as used
% in explorer apps.
% - Expects valsin as V x N matrix where
% V is the number of
% voxels/streamlines/etc and
% ... |
2cf42b9ae83b85a1214b6eb83920059afb19969fc69985a25c86ebd6c3b6f394 | MATLAB | 1,227 | 38 | function yp = swapWithinSubjectLabels(y, subjIdx)
% swapWithinSubjectLabels Restricted permutation for a paired design.
%
% yp = swapWithinSubjectLabels(y, subjIdx)
%
% Independently and with probability 0.5 swaps the two class labels within
% each subject. This is the exchangeability-correct null for a within-s... |
dcc77a37ffb7be64b356187758a25c469bb5f9a3791a6f9411d3f1b304bfe12b | MATLAB | 1,227 | 43 | function value = get(tree,uid,parameter)
% XMLTREE/GET Get Method (get object properties)
% FORMAT value = get(tree,uid,parameter)
%
% tree - XMLTree object
% uid - array of uid's
% parameter - property name
% value - property value
%______________________________________________________________________... |
967fc05c29c64b392ac124c76a2e0f6a7c99094074a4d4853c9a66d94c6db67b | MATLAB | 1,228 | 47 | function obj = geom_interval( obj,varargin )
p=inputParser;
my_addParameter(p,'geom','area');
my_addParameter(p,'dodge',[]);
my_addParameter(p,'width',[]);
parse(p,varargin{:});
obj.geom=vertcat(obj.geom,{@(dobj,dd)my_ci(dobj,dd,p.Results)});
obj.results.geom_interval={};
end
function hndl=my_ci(obj,draw_data,param... |
97c766a8e471e545c902fdd824f81cd5af2b30baeb984dfc5257b83bcda1eb31 | MATLAB | 1,228 | 26 | function ft_struct = Trinh_happe_wavThresh(ft_struct,wavLvl,wavFam,ThresholdRule)
% function uses the wavelet thresholding algorithm from HAPPILEE
% needed input: ft_struct from ft_preprocessing
% wavelevel 10 for sampling rate higher than 500, 9 for 250-500, 8 for
% lower than 250
% Set the wavelet family dependi... |
0c5a5275d2adc18b26eebae55b6f083fb0d5f48d4a00d52a30b942e58c40b060 | MATLAB | 1,229 | 33 | function obj3 = binaryopp(f, obj1, obj2)
if isa(obj2, 'mmo'), tmpobj = obj2; obj2 = obj1; obj1 = tmpobj; clear tmpobj; end;
if ~isequal(size(obj1), size(obj2)) && prod(size(obj2)) ~= 1
error('Matrix dimensions must agree.');
end;
data1 = memmapfile(obj1.dataFile, 'writable', obj1.writable, 'for... |
4f7f41037da263ed350347d98ed5bb09fa6fea967740b23c8c2ef9466ba51448 | MATLAB | 1,229 | 54 | % Demonstration of comparison between two independent groups
%
% SF 2014
clear all
close all
Ntrials = 500;
Nsub = 30;
c = 0;
c1 = [-1.5 -1 -0.5];
c2 = [0.5 1 1.5];
group_d = 2; % same dprime across groups
sigma = 0.5;
group_mratio(1) = 1;
group_mratio(2) = 0.6; % group 2 has worse metacognition than group 1
j... |
c1bff72bea446002119e0a75b8a3f5c2fb057dd085ccc43ada6f7c03818b3925 | MATLAB | 1,229 | 48 | function [rrois, rlookup]= create_rrois (rois, n, Sa, Va, off_set, bind, bl_dir, nz);
% Create a null model == rois with all spatial information removed.
% Compute correlation index for full matrix
% Note that when you start to rotate, the max index of correlation is not necessarily the same any more
% Total number of... |
05ab8c4aca7dc9b2166a97e2af0c515a340efb99d4d4a6a85c5de781993a1a09 | MATLAB | 1,230 | 54 | function f=processBiopac4(bio,tt,desres,skpii)
% Usage ... f=processBiopac4(bio,tt,desres,skpii)
%
% Processing applied to all trials in structure
do_aux=1;
if do_aux&isfield(bio,'AUX3'), do_aux=1; else, do_aux=0; end;
original_flag=0;
dt=tt(2)-tt(1);
tmpii=find(tt>=0);
if isempty(tmpii),
ii0=1;
else,
ii0=tmpii... |
5cbb5561ef04ec84b620dddc08f1befb82d5828a6e0461d632aed9865023c01d | MATLAB | 1,230 | 46 | function [p alpha] = circ_vmpdf(alpha, thetahat, kappa)
% [p alpha] = circ_vmpdf(alpha, w, p)
% Computes the circular von Mises pdf with preferred direction thetahat
% and concentration kappa at each of the angles in alpha
%
% The vmpdf is given by f(phi) =
% (1/(2pi*I0(kappa))*exp(kappa*cos(phi-thetahat)
%
%... |
6febf4a48b1607b3143468d264c483db6de793fb64163b3e12d3826d8f8fda31 | MATLAB | 1,230 | 36 | function [vals,p_vals] = ea_discfibers_weightedLinearRegression(activ_prob, outcome, expected_outcome_metric, output_stat)
% by Till Dembek, publication TBA
% Warning: this metric takes time to be calculated
expected_outcome = zeros(size(activ_prob));
if strcmp(expected_outcome_metric,'mean')
expected_out... |
84411465deca99159234c1e9aadba6ed0108949adb16baeccd3df2e44c938fb3 | MATLAB | 1,230 | 38 | % Closest Toeplitz SDP search.
%
% This script finds a Toeplitz Hermitian PSD matrix that is closest to a
% given Hermitian matrix, as measured by the Frobenius norm. That is, for
% a given matrix P, it solves:
% minimize || Z - P ||_F
% subject to Z >= 0
%
% Adapted from an example provided in the SeDuMi docum... |
9ca7e0b1b14baa112aef0a09b2a887dcf5978d3bae3704e31e1646fa14974842 | MATLAB | 1,230 | 27 | %%*************************************************************************
%% sqlptermcode.m: explains the termination code in sqlp.m
%%
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%***************************************************************... |
256342248147c335001db5dc1c20e744d5e119bd315c6b9c0621f3727acd5f69 | MATLAB | 1,232 | 56 | function y = Insert(x,lines,where)
%Insert - Insert lines in a matrix.
%
% USAGE
%
% result = Insert(matrix,lines,indices)
%
% array matrix where the lines should be inserted
% lines list of values to insert
% indices list of (possibly repeated) matrix line numbers
% ... |
f2d6f1cf6938960bc57c9404ceb1f95ceec3608d922ea7be1aaac50978fdb50c | MATLAB | 1,232 | 37 | function SaveRippleEvents(filename,ripples,channelID)
%SaveRippleEvents - Save hippocampal ripple (~200Hz oscillations) events.
%
% USAGE
%
% SaveRippleEvents(filename,ripples,channelID)
%
% filename file to save to
% ripples ripple info as provided by <a href="matlab:help FindRipples">FindRippl... |
91215cfdc51e9d9cef28065e8ed311563cf48a7607c1e671e54cbaab6b3087ea | MATLAB | 1,233 | 47 | %%% Figure 1A: 10-ms zoom-in spectrogram, log-frequency display
clear; clc; close all;
%% Parameters
f0 = 245; % base frequency, Hz
nHarm = 7;
harmonics = f0 * 2.^(0:nHarm-1); % 245 to 15680 Hz
amp = 1/numel(harmonics);
dur_ms = 100;
t_ms = linspace(0, dur_ms, 700);
% Use log2 frequency co... |
aa8378df0aec144b7b60d7f7c07e13bce1f3904cfcf30ef44c36229dca4b2262 | MATLAB | 1,233 | 43 | %%% export MUA - THINGS dataset
% 2022 P. Papale fecit
clear all
addpath(genpath('\_code\code_utils_v2\'));
% constants
monkey = 'monkeyF';
datadir_gen = '\';
reliab_th = .3;
arrays_to_export = 1:16;
% arrays_to_export(5) = [];
%
filename = [datadir_gen,monkey,'\THINGS_normMUA.mat'];
load(filename)
... |
7e914bcb6f283c519f1a0f4312d31dd2a481beaa8b5b1f56b221588561238f18 | MATLAB | 1,234 | 31 | function [values, oldmin, oldmax] = rescale(values, newmin, newmax)
%RESCALE Rescales a data set.
% [VALUESOUT, OLDMIN, OLDMAX] = RESCALE(VALUESIN, NEWMIN, NEWMAX), given
% a VALUESIN array of arbitrary dimension, will return a VALUESOUT of
% the same size and linearly rescaled to the range NEWMIN:NEWMA... |
38c31828c4d4c95fdba26e07173903ae499b8680b02ae445b698590699236fb1 | MATLAB | 1,235 | 58 | function out = filterAudio(trialdata,ord1,ord2,range)
% load a trial of mic data
% 1000 Hz sample rate assumed
% load(trialname);
% figure; set(gcf,'Position',[200 50 1000 700]); hold on;
% subplot(3,2,1); plot(trialdata); ylim([-0.05 0.1]);
% subplot(3,2,2); spectrogram(trialdata,500,250,'yaxis')
[b... |
6e22083651e056cd3f5d94b49851c745129b597333045876282d7aefa7399ec9 | MATLAB | 1,236 | 37 | function [peak,sprofil] = ea_diode_intensitypeaksFFT(intensity,noPeaks)
%% this function detects 'noPeaks' number of intensity peaks. peaks are constrained to be at 360°/noPeaks angles to each other.
%% Function runs a noPeaks * (360°/noPeaks) array over the intensity-profile and finds the angle at which the su... |
31ea13410707e80c94146f32338c9e406d8a615c619f2a85b376f2859b2a37ce | MATLAB | 1,237 | 34 | function [imgRGB, imgMask, xBounds, yBounds, combinedGrads, cmap] = makeCombinedGradientMap(allROIs, metricFields, gridRes, xLimits, yLimits, cmapInfo, smoothSDPts, smoothSDImg)
% Combines multiple metric maps using the quadratic mean or rms over maps
% Make maps
gradMaps = cell(length(metricFields));
imgMasks = cell(... |
a838613af0c54b5baae08e158583cd0645acf48cac2196979d058fdbb27d6d0a | MATLAB | 1,238 | 43 | % loglike() - log likehood function to estimate dependence between components
%
% Usage: f = loglike(W, S);
%
% Computation of the log-likelihood function under the model
% that the ICs are 1/cosh(s) distributed (according to the tanh
% nonlinearity in ICA). It does not exactly match for the logistic
% nonlinearity, b... |
7215d423bb9c8af92f196651dd99b28085926a0957d62ca509f6987d3c8e032d | MATLAB | 1,239 | 43 | function units = GetUnits(groups)
%GetUnits - Get list of units.
%
% USAGE
%
% units = GetUnits(groups)
%
% group one or more optional electrode groups (default = all groups)
%
% EXAMPLES
%
% all = GetUnits; % list all units
% units = GetUnits(2); % list all units on electrode group 2
... |
0e90da3898d217371b04ecae757215c9995631fb8bbbd46819c04574ac92fe22 | MATLAB | 1,241 | 37 | function [a_array1, b_array1] = generate_connectome_edr(a_array,b_array, lambda, topology, isperiodic)
%GENERATE_CONNECTOME_EDR Summary of this function goes here
% Detailed explanation goes here
if nargin < 5 || isempty(isperiodic)
isperiodic = 1;
end
if ~all(size(a_array) == size(b_array))
... |
5ff11b8b5e34bbb86afa625cc7663833f55a86c6934a73aa922db4af9e712958 | MATLAB | 1,241 | 45 | function plotFOVsCCF(dorsalMaps, allFOVs)
% Plots the ROI centroids colored by areas
% Figure
allenMapSMc(dorsalMaps) % Creates figure by itself
% Paper ready figure/axis formatting
panelwidth = 2.25;
panelheight = 3;
leftoffset = 0.5;
bottomoffset = 0.5;
formatFigure(gcf, panelwidth, panelheight, leftoffset, bottomo... |
eef718b1ca57a1691f7fa4942543d51e2e22b6d50974b062c1345b78a4ad6f1f | MATLAB | 1,241 | 52 | function [wincent,f,y] = ez_spectrogram(x,Fs,win,overlap)
%WORK IN PROGRESS
%NEED to add averaging and correct scaling for graphs
%Measures and displays a spectrogram using ez_powermeasure and the
%short-time FFT technique with a Hann window. x should be a time series
%(row or column vector), Fs is the sample ... |
2ba632b329ce4bdd8c971103fef211dbc21e254c0db58f8d242c3e61ffd31f89 | MATLAB | 1,242 | 39 | % reshape() - reshape of memory mapped underlying array
%
% Author: Arnaud Delorme, SCCN, INC, UCSD, Nov. 2008
% Copyright (C) 2008 Arnaud Delorme, SCCN, INC, UCSD
%
% 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 ... |
83cde554b6bebb865ffc0a6bf4e9290aa1f1d9b2e1e19f7f22890f581944df18 | MATLAB | 1,242 | 45 | % configure file for operations on streamline trackings results
%
% for BATCH EDITOR system (Volkmar Glauche)
%
% File created by Susanne Schnell
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function unring = dti_cfg_unring
niiname = cfg_files;
niiname.tag = 'niiname';
nii... |
b0e52a8af9f46a59833854132db544eb1def5f9c8d0fa01f5122756dcbabb1d5 | MATLAB | 1,242 | 32 | %% control_use_before_def.m
%
% POSITIVE CONTROL for clean/use_before_def.py. Not a runnable analysis.
%
% This file reproduces, in miniature, the failure that motivated the checker:
% an option is READ eight lines above the guard that defines it. In MATLAB this
% dies at the read - "Unrecognized function or variable '... |
f8d69787c11f688eb40ed10211783e91103165b1c04f2c54fae918f92722b488 | MATLAB | 1,242 | 38 | function [ cifti ] = ciftiopen(filename,wbcommand,verbose)
% CIFTI = CIFTIOPEN(FILENAME,WBCOMMAND,VERBOSE)
%
% Open a CIFTI file by converting to GIFTI external binary first and then
% using the GIFTI toolbox
%
% FILENAME is string containing file name to open
% WBCOMMAND is string containing the Workbench command.
... |
079864868c788470d7ecb8e24b18818cf11bad987f36116d6ad072b34ab4bf00 | MATLAB | 1,243 | 50 | function rmAllFilFiles(basedir)
% function rmAllFilFiles(basedir)
%
% This function starts in basedir (or the current directory, if no argument
% is given) and recursively searches through every subdirectory and deletes
% all of the .fil files. The .fil files can be deleted after the ndm_start
% scripts are done.
%
% ... |
89fc7fe6a5efa09429985b883e93820a530498a2ec6d83ccaeace9ddc71a6ec9 | MATLAB | 1,243 | 35 | % Section 7.1.1: Counting problems with Poisson distribution
% Boyd & Vandenberghe "Convex Optimization"
% Joëlle Skaf - 04/24/08
%
% The random variable y is nonnegative and integer valued with a Poisson
% distribution with mean mu > 0. In a simple statistical model, the mean mu
% is modeled as an affine function o... |
8a7b18890c2f439e2687e3d5b8add68b17c77a43ecd4594b0d4bd326e6d777e4 | MATLAB | 1,243 | 35 | function correlations(spikes, useassigns, show)
% CORRELATIONS another temporary utility to show clusters
% CORRELATIONS(SPIKES, [USEASSIGNS], [SHOW]);
if (nargin < 2),
if (isfield(spikes.hierarchy, 'assigns')), useassigns = spikes.hierarchy.assigns;
elseif (isfield(spikes.overcluster, 'assigns')), ... |
4355db91ce14c3118476f3d0c6cf2f4f97f411d478eff103df7a46c12a815da8 | MATLAB | 1,244 | 48 | % Example script for estimating a regression model
%
% Steve Fleming 2018
clear all
Ntrials = 100;
Nsub = 50;
c = 0;
c1 = [-1.5 -1 -0.5];
c2 = [0.5 1 1.5];
group_d = 2;
group_baseline_mratio = 0.8;
sigma = 0.5;
sigma_beta = 0.2;
gen_beta = 0.5;
cov = rand(Nsub,1)';
mcmc_params = fit_meta_d_params;
mcmc_params.estim... |
444491ccac54a8d9de80a0d26008bd9d2c74f63af16aa33a1f80e2b5b025da6e | MATLAB | 1,244 | 39 | % getFolder
%
% Similar to uigetdir except that it will remember the location of the
% last opened folder.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Use plotAverageWaveforms
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Kian Torab
% ... |
c0fbc89ad12954b971e6b51c62a93b6b07777bb6dff84435737232efef29db70 | MATLAB | 1,244 | 48 | % Section 5.2.5: Mixed strategies for matrix games
% Boyd & Vandenberghe "Convex Optimization"
% Joëlle Skaf - 08/24/05
%
% Player 1 wishes to choose u to minimize his expected payoff u'Pv, while
% player 2 wishes to choose v to maximize u'Pv, where P is the payoff
% matrix, u and v are the probability distributions of... |
d1e69e5623303dc12c7fc1a14b9fe4029f47563b5887dc57135857ce36aa64e2 | MATLAB | 1,244 | 34 | function LC_pvals = myPLS_get_LC_pvals(Sp_vect,S,pls_opts)
% This function computed pvalues for all latent components (LCs) using the
% permuted singular values
%
% Inputs
% - Sp_vect : L x #permutations matrix, L is #LCs, permuted singular values,
% used to compute p-values to assess LCs' signific... |
eaeeb3707793a3f4bb11e8094315506ea778a5d0c0b420d6792d62af28ee6a7f | MATLAB | 1,244 | 33 | function y = palm_isoctave
% Test whether the function is running in OCTAVE or not.
% Retuns 1 (true) if yes, 0 (false) otherwise.
%
% _____________________________________
% Anderson M. Winkler
% FMRIB / University of Oxford
% Jan/2012
% http://brainder.org
% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ... |
c7143b6ac24a94a5b6d791d9bdf76935c392752b7ccc799de883beb5bc04d6b8 | MATLAB | 1,245 | 34 | function Y4d = palm_conv2to4(Y2d,siz)
% Convert a 2D array (t,x*y*z) into a 4D dataset (x,y,z,t)
%
% Usage:
% Y4d = conv2to4(Y2d,size3d);
%
% _____________________________________
% Anderson M. Winkler
% FMRIB / University of Oxford
% Sep/2012
% http://brainder.org
% - - - - - - - - - - - - - - - - - - - - - - - - -... |
6b573f0f2e21dd220a818efaac69571183c03b76747e9304ae6674b3934f1095 | MATLAB | 1,246 | 38 | function r = trirnd(varargin)
%TRIRND Pseudorandom numbers drawn from the triangular distribution
%
% R = IOSR.STATISTICS.TRIRND(N) returns an N-by-N matrix containing
% pseudorandom values drawn from the triangular distribution constrained
% to (-1,1) and mode = 0.
%
% IOSR.STATISTICS.TRIRND(M,N) or IOSR.S... |
86bd229ed3741a820fd0d84190be30b7b8d92242478dcc3c4f023785433fb4db | MATLAB | 1,246 | 36 | %% get data for Kragel et al. 2018 from neurovault
[files_on_disk, url_on_neurovault, mycollection, myimages] = retrieve_neurovault_collection(3324);
FullDataSet=fmri_data(files_on_disk);
%% Extract information about study (1-18) and subject number
reorder_studies_and_subjects;
%% Get masks from brainnetome atlas
bn_a... |
0121fda208e422528b611dbcc20574f103647e55fd871db30a60435ec6755dbd | MATLAB | 1,247 | 50 | %%******************************************************************
%% blkcholfun: compute Cholesky factorization of X.
%%
%% [Xchol,indef] = blkcholfun(blk,X,permX);
%%
%% X = Xchol'*Xchol;
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*******... |
268c37b695e6af648decc71ef3d68ca193c831ef69ffee8fa6b328a2b51c338e | MATLAB | 1,247 | 31 | % eventalign - function called by pop_importevent() to find the best
% sampling rate ratio to align 2 arrays of data events.
%
% Author: Arnaud Delorme, SCCN/INC/UCSD, Dec 2003
% Copyright (C) Arnaud Delorme, CNL / Salk Institute, 9 Feb 2002, arno@salk.edu
%
% This program is free software; you can redis... |
6769818efaa2cd802ae216c5ad3e5fd908f09d7273018cef1f0f2ca969c29373 | MATLAB | 1,247 | 29 | function [r] = sample_inverse_gaussian(mu,lambda)
% This file is a part of the MDSINE program.
%
% MDSINE: Microbial Dynamical Systems INference Engine
% Infers dynamical systems models from microbiome time-series datasets, and
% predicts biologically relevant behaviors of the ecosystems.
% Copyright (C) 2015 Vanni... |
b19e457682ba23b2d263f1c6a5132365b0ea3810271081b1ab6ca97169636f16 | MATLAB | 1,247 | 39 | function ea_convert_synthSeg2segmask(SynthSeg_segmask_image, segmask_output)
% convert SynthSeg segmentations to GM/WM/CSF
% IMPORTANT: lesions are not segmented, check for atrophies beforehand
SynthSeg_segmask = ea_load_nii(SynthSeg_segmask_image);
% initialize
Segment_GM_WM_CSF = SynthSeg_segmask;
% change the na... |
f5150655623c03dbbb15ac9376553795ac83072a5470be4aa4bcf9be22c498cb | MATLAB | 1,247 | 42 | function peaks = localpeaks(x,mode)
%LOCALPEAKS Find local peaks and troughs in a vector
%
% This function returns the indices of local peaks and/or troughs in a
% vector.
%
% PEAKS = IOSR.DSP.LOCALPEAKS(X) locates the local peaks in vector X.
%
% PEAKS = IOSR.DSP.LOCALPEAKS(X,MODE) locates local features spec... |
087f4b83e4df701dbf909df43bd60d3d486001dcc2090f8b984a18b0241372f9 | MATLAB | 1,248 | 50 | function AUC = quickGroupedCV(X, Y, subjIdx, C, K, opts)
% quickGroupedCV Subject-blocked grouped CV for the paired PLS-DA permutation null.
%
% AUC = quickGroupedCV(X, Y, subjIdx, C, K, opts)
%
% Folds are formed over SUBJECTS, so both observations of a subject always
% land on the same side of the split. Pass ... |
a7cc254a09cae68c0f1473701f4ae975bde382d01d87df41fa32707a6b60f1a2 | MATLAB | 1,248 | 44 | function write_cifti(data, varargin)
%
% Usage:
% write_cifti(data, varargin)
%
% Description:
% Writes cifti file (authors: @NicoleEic, @saratheriver)
%
% Inputs:
% data (single or double) - Data to be saved
%
% Name/value pairs:
% dpath (string, optional) - Path to location for saving file
% (e.g., '... |
e0a632d42c40e524e79cd85bacafc767c1297be1845b40a1798e37a17c9e1fdd | MATLAB | 1,248 | 40 | function [accuracy, confusion_matrix] = eval_train(pred_fname)
% Evaluates training accuracy.
% Arguments:
% pred_fname: Filename of prediction file for training. The required format
% is described in the README.
% Returns:
% accuracy: The accuracy on the training set.
% confusion_matrix: The confusion matrix... |
1b2a2d68c7b9fb583f9cb616fbf95728164070a02f366972e30781223e0bbb84 | MATLAB | 1,249 | 45 | function checkfits(headpath,fileexpnum,imskip,expskip)
cd(headpath);
filelist=dir;
[Xpix,Ypix,FrameRate]=findkeyparams();
disp('select the mat file from the experiment from this computers C drive');
[matexpfile,matexppath]=uigetfile('*.*');
cd(matexppath);
load(matexpfile);
cd(headpath)
%add some errorchecking for in... |
21d6c7e581fd681e2135444eca78a59d0449827a66f8b9e7d65cb601a8f3849a | MATLAB | 1,249 | 52 | function P = setup_paths()
%FNIRSPOWER.SETUP_PATHS Add fnirspower and third-party dependencies to the MATLAB path.
%
% P = fnirspower.setup_paths()
%
% Adds:
% - fnirspower MATLAB root
% - selected third-party dependencies
%
% Notes
% -----
% - FieldTrip is added only at the top-level folder. Call... |
55d52e7030d513f162e616a9db30e4b5540a2588a331d8d7224d0d58161bfe3c | MATLAB | 1,249 | 53 | function ea_bet(inputimage, outputmask, outputimage, fraintthreshold)
% Wrapper for bet2 brain extraction
% Do not output brain mask by default
if nargin < 2
outputmask = 0;
end
% overwrite the input image
if ~exist('outputimage','var')
outputimage = inputimage;
else
if isempty(outputimage)
output... |
5bc394d20248d44601230beda10edf3615eb1c61568d00f421160ac20308752a | MATLAB | 1,249 | 57 | function y = hsl2hsv(x)
%hsl2hsv - Convert hue-saturation-luminance colors to hue-saturation-value.
%
% USAGE
%
% y = hsl2hsv(x)
%
% x Nx3 RGB matrix (values in [0..1])
% Copyright (C) 2013 by Michaël Zugaro
%
% This program is free software; you can redistribute it and/or modify
% it under the te... |
6f258af260a7a37295bca7dd1f1ebf8f2a905442aaafd60ab3683d5044c9a3f3 | MATLAB | 1,249 | 32 | function ClincFreq_Norm2MNI_T1_clinc(indat,inroi,outdir,outname,voxelsize,pth)
try
[patdat,namdat,extdat] = fileparts(indat);
% [patroi,namroi,extroi] = fileparts(inroi);
% load([pth,filesep,'Norm2T1_segment.mat']);
load([pth,filesep,'Norm2T1_clincal.mat']);
pathspm = which('spm.m');
[patspm,namspm,extspm] = fileparts... |
715ec4fb20ce9fed1b3e80a1d50cc794b3eea219f826dcfa56941f145e2191dc | MATLAB | 1,249 | 40 | function p=internalpoint(v,aloop)
%
% p=internalpoint(v,aloop)
%
% imperical function to find an internal point
% of a planar polygon
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2008/04/08
%
% input:
% v: x,y,z coordinates of each node of the mesh
% aloop: input, a single vector separated by Na... |
f949d5595fbc0b480e790cc751148463b92796571d0aa97b14fc3b96f32e3494 | MATLAB | 1,249 | 30 | % spherror() - chancenter() sub function to compute minimum distance
% of Cartesian coordinates to a sphere
%
% Author: Scott Makeig, CNL / Salk Institute, 2000
% Copyright (C) Scott Makeig, CNL / Salk Institute, 2000
%
% This program is free software; you can redistribute it and/or modify
% it under the... |
c9eff667d2819f551df96fb074ce9beb766c276e723dde8feffb9da76a45aaa8 | MATLAB | 1,250 | 42 | function p=speed_kalman(x,y, fs_video)
defpars=[50 .02 .01 100 2 .1 10];
if ~exist('pars','var')
pars=defpars;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%% pos estimation
% pars=[100 1 .03 1000];
% pars=[100 50 1 1000];
% pars=[108.2592 52.2000 0.9360 762.8400];
R... |
6d1c0b07bd3b77b3fc6755f0586f5cd1aa46745e0344e75c5ceacea4c28e3e5e | MATLAB | 1,251 | 48 | function plotSubpopAreaProportions(allROIs, areas)
% Plot stacked bars indicating the proportion of each subpopulation within
% each area
% Make figure
fig;
% Set sizes
% Paper ready figure/axis formatting
panelWidth = 1.16;
panelHeight = 2.16; % This is the only way to get the right aspect ratio from the first submi... |
97de2ec37a117da17b9aa973f7250d2ef839f6f05e470e3f8d66177043b042dd | MATLAB | 1,252 | 41 | function info = BatchInfo(batch)
%BatchInfo - Get batch job information.
%
% USAGE
%
% info = BatchInfo(batch)
%
% batch batch parameter returned by <a href="matlab:help StartBatch">StartBatch</a>
%
% OUTPUT
%
% info.mfile batch function
% info.data batch data
% info.done whethe... |
bffa41aaca82700ff7fc962f708a083e27e3275303a419d6e602180e2287e77d | MATLAB | 1,252 | 39 | function ea_checkleaddirs
prefs=ea_prefs;
if ~isfolder(prefs.lc.datadir)
if ~(isdeployed && ~isfield(prefs,'firstrun')) % don't enter first time in deployed app
try
ea_mkdir(prefs.lc.datadir);
catch
ea_cprintf('CmdWinWarnings', 'Failed to create connectome directory.\nPlease... |
34f771829bdf94cdbaa1fc8a81320b4f45a1cc2543bbe937eca9f07835c550be | MATLAB | 1,253 | 28 | function ea_genctmask(options)
masks_path = fileparts(options.subj.recon.rawCTMask);
ea_mkdir(masks_path);
if ~isfolder(masks_path); mkdir(masks_path); end
copyfile([ea_space,'brainmask.nii.gz'], fullfile(masks_path,'brainmask.nii.gz'));
gunzip(fullfile(masks_path,'brainmask.nii.gz'));
ea_delete(fullfile(masks_path,... |
458527807f3fa3cd900181e4b736bad0b605084477fdfa311366e9985c2fc982 | MATLAB | 1,253 | 46 | function [d pred] = dag_sp(A,u,varargin)
% DAG_SP Compute the weighted single source shortest path problem.
%
% The DAG shortest path algorithm for the single source shortest path
% problem only works on directed acyclic-graphs (DAGs).
%
% If the graph is not a DAG, the results are undefined. In the future, the
% fu... |
46b203fbe53ab04c05066932c9126e35d9f06631c4fca25f83a0248b866a0e0e | MATLAB | 1,253 | 47 | function savemedit(node,face,elem,fname)
%
% savemedit(node,face,elem,fname)
%
% save a surface or tetrahedral mesh to Medit format
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2010/10/30
%
% input:
% node: input, surface node list, dimension (nn,3 or 4)
% face: input, surface face element list, dim... |
27eb82e1b57af5edd28fc75314d5223e5292fe454fb4704c488e1571ab4fc072 | MATLAB | 1,254 | 32 | function [res] = LCN_cost_intact_tracer_hill(params)
%
% costfunction for the calculation of the intact fraction of a tracer
% using a Hill function (see LCN_calc_intact_tracer_hill.m)
% We don't assume that at time t=0, the intact fraction is 1, but allow
% a delay before metabolites appear
%
% FORMAT: res = LCN_cost... |
667f0e1fe4a4d13f3083af7b9e02690fdc842c73ea457b0f216b3cba29a35add | MATLAB | 1,254 | 49 | function saveConcatMat(genotype,thedata,trllength)
% example inputs:
% thedata = 'nov1122_f1e4';
% trllength = 106;
% genotype = 'VT062617';
% First, navigate to the folder containing the folders of data you want to
% concatenate.
[Xpix,Ypix,FrameRate,Zframes]=findkeyparams_newThor5D();
FrameRate=str2doub... |
8cd7931e98937c244c237bd740fbf37139fe42c366269f365629f1f221bc6af6 | MATLAB | 1,254 | 26 | function [n,adchans] = plx_ad_chanmap(filename)
import CMBHOME.PLX2Mat.*
% plx_ad_chanmap(filename) -- return map of raw continuous channel numbers for each channel
%
% [n,adchans] = plx_ad_chanmap(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% OUTPUT:
% n - number of continuous cha... |
9e2d94aaa5bb75415dfbd8aac0bb0a194be09f98637220258004bdacda941834 | MATLAB | 1,254 | 33 | function splitData(params)
% splitData(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 Information Pro... |
b8c2bde246029a241c2ccadb491d8a2fbe3738dc76e1b27d7531d92dd37a7342 | MATLAB | 1,254 | 44 | function trainedML = train_RF_matlab(database_train, params_train, n_trees, SANDIinput)
% Train a Random Forest regressor for SANDI fitting
%
% Author:
% Dr. Marco Palombo
% Cardiff University Brain Research Imaging Centre (CUBRIC)
% Cardiff University, UK
% 8th December 2021
% Email: palombom@cardiff.ac.uk
tic
train... |
bfaecdbfa77fea151ddc03057aa18421342e354db35645f18dab34dfbb5ebe48 | MATLAB | 1,254 | 27 | function settings = ea_load_prob_parameter(options, settings, outputPaths, sideCode, sample_i)
% Load probabilistic sample
% IMPORTANT:this is a special case for multisource prob. PAM
% By Butenko, konstantinmgtu@gmail.com
arguments
options % Lead-DBS options for electrode reconstruction and stimulati... |
3433ef7819080907e53d8001d02b1ed8bce3b2e7d675a0b9bf3d38f80e5ace76 | MATLAB | 1,255 | 36 | function [numDICOM, fileList, isCompressed] = ea_dcmquery(input, queryOption)
% Check the number of DICOM file(s) in the specified folder
%
% queryOption can be 'y' (only show number of DICOMs found) or 'l'(show
% number of DICOMs found and list of DICOMs)
arguments
input {mustBeFolder}
queryOption {mustBeMemb... |
451b4dcd8426bd953c6162d7ac92ce3df67396dcfc8910cb5388507d05863fb2 | MATLAB | 1,255 | 43 | function runIntersect = mintersect(varargin)
%MINTERSECT Multiple set intersection.
% MINTERSECT(A,B,C,...) when A,B,C... are vectors returns the values
% common to all A,B,C... The result will be sorted. A,B,C... can be cell
% arrays of strings.
%
% MINTERSECT repeatedly evaluates INTERSECT on succes... |
23fb4db420c954e04594fc806bac6cf8cefbf7cb61514e972a529e18076e1154 | MATLAB | 1,256 | 42 | function z = matrix_frac( x,Y )
%MATRIX_FRAC Matrix fractional function.
% MATRIX_FRAC(x,Y), where Y is a square matrix and x is a vector of the
% same size, computes x'*(inv(Y)*x) if Y is Hermitian positive definite, and
% +Inf otherwise.
%
% An error results if Y is not a square matrix, or the size... |
bbea941a11c492932d1f1ed9c56bcbabe6d5cfda91e7ef3e70d1c818906e17cf | MATLAB | 1,256 | 36 | function my_system(command)
%like call_fsl, but without sourcing fslconf
if ismac()
ldsave = getenv('DYLD_LIBRARY_PATH');
%this is just a guess at what matlab does on mac, based on using LD_PRELOAD on linux
presave = getenv('DYLD_INSERT_LIBRARIES');
macflatsave = getenv('DYLD_FOR... |
d18d8cdbdfa110e6e09bb27dd698203776d4f7317567c0fc8ab45c1acd31b17f | MATLAB | 1,256 | 35 | function [w,rho] = best_const(A)
% Computes the constant edge weight that yields fastest averaging.
%
% [W,RHO] = BEST_CONST(A) gives a vector of the best constant edge weights
% for a graph described by the incidence matrix A (NxM). N is the number of
% nodes, and M is the number of edges. Each column of A has exactly... |
1ca3e10d56bad1bdaa0d2443c85c39d10b184217b9564199867ef6110abffcc6 | MATLAB | 1,257 | 39 | function params = parseVarArgs(params,varargin)
% Parse variable input arguments supplied in name/value format.
%
% params = parseVarArgs(params,'property1',value1,'property2',value2) sets
% the fields propertyX in p to valueX.
%
% params = parseVarArgs(params,varargin{:},'strict') only sets the field
%... |
b7d39d360a134bb64637a906681eb0383e55b016995d490faa606db48998cf16 | MATLAB | 1,257 | 26 | function z = kl_div( x, y )
%KL_DIV Scalar relative entropy.
% KL_DIV(X,Y) returns an array of the same size as X+Y with the Kullback-
% Leubler divergence function applied to each element:
% { X.*LOG(X./Y)-X+Y if X > 0 & Y > 0,
% KL_DIV(X,Y) = { 0 if X == 0 & Y >= 0,
% ... |
edace5caf354220b8e445a0c266d4abf8941e758a053843b03519f7d4dc320be | MATLAB | 1,258 | 47 | function [p alpha] = circ_vmpdf(alpha, thetahat, kappa)
% [p alpha] = circ_vmpdf(alpha, w, p)
% Computes the circular von Mises pdf with preferred direction thetahat
% and concentration kappa at each of the angles in alpha
%
% The vmpdf is given by f(phi) =
% (1/(2pi*I0(kappa))*exp(kappa*cos(phi-thetahat)
%
%... |
45d19feb595154adc8ef4b3de09d168cb47049f62b86f56647255f0cd2b31ac6 | MATLAB | 1,260 | 28 | function [parmstype2] = convertGSASparms(parmstype1,numcells,numAS)
%UNTITLED3 Summary of this function goes here
% Detailed explanation goes here
% If structure, returns vector (for use in fitting algorithms).
% If vector, returns structure, (needs numcells, numAS)
%Note: vectr form uses logCV... for fitting bounds ... |
c65b0ce73ee55ac11824e60b8508b90e17d4a7de55d7e3a4f5644bdb2c35a70e | MATLAB | 1,260 | 54 | function savevrml(node,face,elem,fname)
%
% savevrml(node,face,elem,fname)
%
% save a surface mesh to VRML 1.0 format
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2010/04/25
%
% input:
% node: input, surface node list, dimension (nn,3)
% face: input, surface face element list, dimension (be,3)
% ... |
0a5f4532ea4e3aea045253cf67eb2034b1209a7327782a288758ae2c796b4496 | MATLAB | 1,261 | 40 | function [ w, cvx_optval ] = fmmc(A)
% Computes fastest mixing Markov chain (FMMC) edge weights
%
% [W,S] = FMMC(A) gives a vector of the fastest mixing Markov chain
% edge weights for a graph described by the incidence matrix A (n x m).
% Here n is the number of nodes and m is the number of edges in the graph;
% each... |
d1fb49dc3ae7e2afe783260da2e2110cc6201c18d0ae1b5a5ff38ff58c12f3b5 | MATLAB | 1,261 | 52 | function h = PhasePlot(x,y,phase,sz,varargin)
% Plots arrows indicating the phase on current axis.
%
% [h,yy,zz] = PhasePlot(x,y,phase,sz[,ArrowParameters])
%
%
% Requires the Arrow function by Erik A. Johnson.
%
% Note: Arrows will get skewed if you resize the axis.
%
% Aslak Grinsted 2003
% ---------... |
70fc28e5288f1a510c931e89d2903af490d61edac381e8f2d6b5b79b91f012f3 | MATLAB | 1,262 | 27 | function [] = intersectROIfiles(dataPath,animal,filters,tifList,tifFiles)
for ROIfileN = 1:length(filters)
preROI{ROIfileN} = load(fullfile(dataPath,[animal '_moCorrROI_' filters{ROIfileN} '.mat']),'moCorROI');
ROIids{ROIfileN} = string({preROI{ROIfileN}.moCorROI.ID}');
end
allROI = vertcat(ROIids{:}... |
c4555ce1c4f59b4c50941feda54817cdffe433b0d489fa85643da19617b88ff3 | MATLAB | 1,262 | 56 | function cleanimg=deislands2d(img,sizelim)
%
% cleanimg=deislands2d(img,sizelim)
%
% remove isolated islands on a 2D image below speicified size limit
%
% author: Qianqian Fang (fangq <at> nmr.mgh.harvard.edu)
%
% input:
% img: a 2D binary image
% sizelim: a integer as the maximum pixel size of a isolated region
%
% ... |
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