sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0b67fdc319806aef46a6d3d774d906d901c4940b184a576287a089b38c6afe7a | MATLAB | 650 | 20 | function y = square_pos( x )
%SQUARE_POS Square of positive part.
% SQUARE_POS(X) is the square of the postive parts of the elements of X;
% i.e., SQUARE_POS(X)=MAX(X,0).^2. X must be real.
%
% Disciplined convex programming information:
% SQUARE_POS(X) is convex and nondecreasing in X. Thus when used i... |
5314a43476ffb1775d6662bcb63ebd70ab67e1986de04ae85c79e92b1cb6e45f | MATLAB | 650 | 27 | RandPhi = 2 * pi * rand(100000,1);
RandTheta = pi * rand(100000,1);
RandPts = [cos(RandPhi), sin(RandPhi).*cos(RandTheta), sin(RandPhi).*sin(RandTheta)];
tic
[tmp, tmp, TreeRoot] = kdtree(RandPts, []);
TestPhi = 2*pi*rand(100,1);
TestTheta = pi*rand(100,1);
TestPts = [cos(TestPhi), sin(TestPhi).*cos(TestThet... |
dd4cbc126828682a5c10e0a2d4a68ef4a5aed6f8dbe013f8e51fa7aad0c1bc42 | MATLAB | 650 | 18 | %this function loads a scanimage type tif but ignores metadata
%this doesn't handle 2 channel tifs
function justImgData = justLoadTif(TifFile)
tifInfo = imfinfo(TifFile);
nFrames = length(tifInfo);
warning('off','MATLAB:imagesci:tiffmexutils:libtiffWarning');
warning('off','imageio:tiffmexutils:libtiffWarning');
... |
de1b0437b70277d30b7cffbc0ef921976339f25ea962a3b916354a434b970a33 | MATLAB | 650 | 19 | function [HR, bad, nCh] = estimate_hr_snr_bad(dOD_hp, Fs, snr_thr)
%NIRSPROC.ESTIMATE_HR_SNR_BAD HR (Hz) from spectrum and SNR-based bad channels.
% [HR, bad, nCh] = ESTIMATE_HR_SNR_BAD(dOD_hp, Fs, snr_thr)
% channel count per wavelength
nCh = size(dOD_hp,2)/2;
[freq,amp] = get_spec(Fs, mean(dOD_hp(:, std(dO... |
24446ac96754e64b70f61254dc7939141a6a9c7cf6b7641a11aa992d2dd159ff | MATLAB | 651 | 36 | function truefalse = ch_eqi ( c1, c2 )
%*****************************************************************************80
%
%% CH_EQI is a case insensitive comparison of two characters for equality.
%
% Example:
%
% CH_EQI ( 'A', 'a' ) is TRUE.
%
% Licensing:
%
% This code is distributed under the GNU LGPL licen... |
f8c4b92413bdffc976ac0ed72f145a27cf28ea95b0d6a95f90f8eb562c0bc324 | MATLAB | 651 | 26 | function [wMean, wStdDev] = CBIG_compute_weightedMeanStdDev(X, y)
% [wMean, wStdDev] = CBIG_compute_weightedMeanStdDev(X, y)
%
% Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
no_subtypes = size(X, 2);
%--------- Compute weighted mean
wMean = zeros(1, no_subtypes);
fo... |
a49f05150d70208f5e5f08e675ada6f44eda0a597b32ecb5b7272d2436bfbd43 | MATLAB | 653 | 18 | function s = char(tree)
% XMLTREE/CHAR Converter function from XMLTree to a description string
% FORMAT s = char(tree)
%
% tree - XMLTree object
% s - a description string of an XMLTree
%__________________________________________________________________________
%
% Return a string describing the XMLTree:
% ... |
20bd1716887c6a148f2f705acd882cf8b52927afefa8a363d5f1d89743b24ca4 | MATLAB | 655 | 25 | %%***************************************************
%% qprod:
%%
%% Input: A = [A1 A2 ... An]
%% x = [x1; x2; ...; xn]
%% Output: [A1*x1 A2*x2 ... An*xn]
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%**************************************... |
2ba9da755c98548a3514000d7dd3f215341a88de890acc42310ba5fcbeffcd25 | MATLAB | 655 | 30 |
function [p,s] = project2surf_V7(p,s, subnr)
% [p,s] = project2surf(p,s, subnr)
%
%
%
%setenv('FREESURFER_HOME','/home/inverse/freesurfer/freesurfer')
Hemis={'lh', 'rh'};
FS_surfDir = fullfile(p.FS_subDIR, p.subNames{subnr}, 'surf');
% make cellarray with scannames
scanlist = cell(1,2);
for ii = 1:length(p.ppscanNam... |
bbe00bad6d2617fa6779180c30392d3b8a88d986e3ec4a13f144e0729fbf84a6 | MATLAB | 655 | 18 | function [handles] = get_spineROImask(handles)
roi_mask = zeros(size(handles.im_norm));
handles.size = size(handles.im_norm);
if ~isempty(handles.roi)
if size(handles.roi,3) ~= size(handles.spine_trace,2)
waitfor(msgbox('Number of trace and number spine ROI inconsistent',...
'Warning', 'warn'))... |
4bd3eec14d14776cd51ae319e5a8136d22a43816a0cf31ba96d60c5aea85d2f4 | MATLAB | 656 | 28 | function [A,sumV] = quadcof(N,NW,order)
% Helper function to calculate the nonstationary quadratic inverse matrix
% Usage: [A,sumV] = quadcof(N,NW,order)
% N (number of samples)
% NW: Time bandwidth product
% order: order (number of coefficients, upto 4NW)
%
% Outputs:
%
% A: quadratic inverse coefficient ... |
c987923b1f7a21ec774c2604f3457f142708ac50452036b35528d619ffdaccb7 | MATLAB | 656 | 23 | function [labels_cell, Z] = frid_edit_multiple_k(X,k_list,H,alpha)
num=size(X,1);
[r,~]=size(H);
options = optimset( 'Algorithm','interior-point-convex','Display','off');
A=2*alpha*eye(r)+2*H*H';
A=(A+A')/2;
B=X';
parfor ji=1:num
ff=-2*B(:,ji)'*H';
ff = double(ff);
Z(:,ji)=quadprog(A,ff',[],[],[],[],-on... |
476497d35b53d6bd2b974d06eae3ec2f1638b3989c7a4c8d4234dccdd6ee1317 | MATLAB | 658 | 24 | % Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
% reorient all images in the raw folder
spm_tool_dir = [spm_dir '/toolbox/OldNorm/']
addpath(spm_dir)
addpath(spm_tool_dir)
% roughly translate the image
x = load(reorient_sample);
f = strtrim(image_path);
N ... |
bd2aa057b89012f163461876c6936865d51d78e7f66e35e4b980455a1679b9a9 | MATLAB | 658 | 22 | function model = fitAllROIsGMM(allROIs, metricField, options)
% Fits Gaussian mixture model distributions to all feature vectors, area
% agnostic
% Get metrics z-scored for all neurons
switch metricField
case 'PCs'
metrics = cat(1, allROIs.PCs);
metrics = metrics ./ std(metrics); % z-score
case... |
62dcd80e52832706d7cc65fa5e51c6e7502b684421e5763e865aec8fcb1ab9ca | MATLAB | 659 | 25 | function [y] = cut_line_to_pieces(x, nperpiece)
% File: cut_line_to_pieces.m
% Author: Ioannis Filippidis, jfilippidis@gmail.com
% Date: 2012.06.21 -
% Language: MATLAB R2012a
% Purpose: calculate vertex groups to break a line into multiple segments
% Copyright: Ioannis Filippidis, 2012-
[nrow... |
e7143c887bef25b2cc371b9eac6bbe7ee0d8a02e20693db4b5c4ccf713637d52 | MATLAB | 659 | 31 | function nodevol=nodevolume(node,elem)
%
% nodevol=nodevolume(node,elem)
%
% calculate the Voronoi volume of each node in a simplex mesh
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2009/12/31
%
% input:
% node: node coordinates
% elem: element table of a mesh
%
% output:
% nodevol: volume values... |
05524df0c48d00db7d9878056ae9fd6ac43e92c2a37f3b4175cf819fa7bf610b | MATLAB | 661 | 22 | function display(tree)
% XMLTREE/DISPLAY Command window display of an XMLTree
% FORMAT display(tree)
%
% tree - XMLTree object
%__________________________________________________________________________
%
% This method is called when the semicolon is not used to terminate a
% statement which returns an XMLTree.
%_____... |
803572ef40b914baf5270bfee048a168bf3639100264f948a0889e51d3b7d231 | MATLAB | 663 | 18 | function [adfreq, n, ad] = plx_ad_span_v(filename, ch, startCount,endCount)
import CMBHOME.PLX2Mat.*
% plx_ad_span_v(filename, channel): Read a span of a/d data from a .plx file
%
% [adfreq, n, ad] = plx_ad_span_v(filename, ch,startCount,endCount)
%
% INPUT:
% filename - if empty string, will use File Open dialog
% ... |
9e16a65e13eef525b2477ee1e4d5b3542ff5d1d8d67341a05d1855cc67c1b480 | MATLAB | 663 | 19 | function metadata = cifti_metadata_set(metadata, key, value)
%function metadata = cifti_metadata_set(metadata, key, newvalue)
% Set the value for a specified metadata key.
%
% >> cifti.metadata = cifti_metadata_set(cifti.metadata, 'Provenance', 'I made this');
if ~isstruct(metadata)
... |
a15ab36d244b85aedcf95fa8dd28a5f773ea1dfc86d81473347a8678a973e816 | MATLAB | 663 | 22 | function [ normalised ] = normalise( map )
% [ normalised ] = normalise( map )
%
% ----------------------------------------------------------------------
% Matlab tools for "Predicting human gaze beyond pixels," Journal of Vision, 2014
% Juan Xu, Ming Jiang, Shuo Wang, Mohan Kankanhalli, Qi Zhao
%
% Copyright (c... |
ae8e22bc17b430b8ad19ff524073becf88e85964832352994cfa796ef58844d8 | MATLAB | 664 | 25 | function plot_rsa_results(stats)
figure;imagesc(stats.RDM); colorbar;
xlabel 'Subject Number'; title 'Brain RDM'
%show bootstrap distribution for generalization indices
figure;
subplot(3,1,1)
distributionPlot(stats.bs_gen_index(:,2:19));
title 'Study'
ylabel 'Generalization Index'
subplot(3,1,2)
distributionPlot(st... |
cc9c90908cbbfe8a86f78f8680a953a344510d8f99956038cacaafb17b0113e1 | MATLAB | 664 | 22 | function [newnode,newface]=surfreorient(node,face)
%
% [newnode,newface]=surfreorient(node,elem)
%
% reorder nodes in a single closed surface to ensure the norms of all
% triangles are pointing outward
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2012/07/06
%
% input:
% node: list of nodes
% face: list ... |
fafcb928262ed79d673bece00d80f32f54e9565aafdf83b51fc563815756594d | MATLAB | 664 | 22 | % feature_calc_script
tmp=dir;
nfiles=length(tmp);
names=cell(nfiles,1); for j=1:nfiles, names(j)=cellstr(tmp(j).name); end;
wavnames=regexp(names,'.*wav$','match');
ind=~cellfun('isempty',wavnames);
wavnames=wavnames(ind);
segnames=regexp(names,'.*wav.seg.txt$','match');
ind=~cellfun('isempty',segnames);
segnames=se... |
63d92fc77a1dc2751e3d1f1cb0508ce489051d398aef8acf9da1f516db157e0a | MATLAB | 665 | 25 | function g=aicplot(alpha,varargin)
%
% Computes and plots the -2*AIC
% for local fits with different smoothing parameters.
%
% The first argument to aicplot(), alpha, should be a matrix with one
% or two columns (first column = nearest neighbor component, second
% column = constant component). Each row of this matrix i... |
aae936c201af1c0587a82beae788f11a792a541cd981e75223c9f37be09de0b3 | MATLAB | 665 | 19 | function flip = spm_flip_analyze_images
% Do Analyze format images need to be left-right flipped? The default
% behaviour is to have the indices of the voxels stored as left-handed and
% interpret the mm coordinates within a right-handed coordinate system.
%
% Note: the behaviour used to be set in spm_defaults.m, but t... |
bc188f9d55c7918014bc2196d6723138b5e9740e010643a76dbde4de3a9dd1f8 | MATLAB | 665 | 19 | function z = lambda_min( Y )
% LAMBDA_MIN Minimum eigenvalue of a symmetric matrix.
% For square matrix X, LAMBDA_MIN(X) is MIN(EIG(X)) if X is Hermitian
% or symmetric and real; and -Inf otherwise.
%
% An error results if X is not a square matrix.
%
% Disciplined convex programming information:
% ... |
fad26c22e60bad1d89686d6f06e3d1135baaaa31ec8428e6cdf3cc5b7920724a | MATLAB | 665 | 27 | function [xx,yc]=mydftreg_vol(im,refim,parms)
% Usage ... [x,imc]=mydftre_volg(vol,volref,parms)
%
% parms=[scalef smwid]
upscalef=parms(1);
smw=parms(2);
if nargout==0, verbflag=1; else, verbflag=0; end;
if length(parms)==3, verbflag=parms(3); end;
for mm=1:size(im,4),
im1=refim;
im2=im(:,:,:,mm);
... |
832488287ff3818a5ec450c8eaad36ef6e2f130ffffd15a07f7fdb8f4b4dabdd | MATLAB | 666 | 16 |
connMap = imread('Empty.tiff');
% Create all reference nodes
for node = 1:size(channelPos,2)
if sum(contains(electroSele, electrodes{node})) ~= 0
connMap = insertShape(connMap,'FilledCircle',[channelPos(1,node) channelPos(2,node) 5],'Color',[0 127 127]);
connMap = insertText(connMap, [channelPos(1,node)+5... |
83ffb1fb03a190f423f6c37253cee820801e41838d52f6c7ac8da3e1dd43fd0f | MATLAB | 666 | 21 | function ea_lcm_struc(options)
if strcmp(options.lcm.struc.connectome,'No structural connectome found.')
return
end
disp('Running structural connectivity...');
useNativeSeed = options.prefs.lcm.struc.patienttracts.nativeseed;
if strcmp(options.lcm.struc.connectome, 'Patient''s fiber tracts')
connBaseFolder = ... |
20e56c43dd7afc75813fd89f731e49876b55d961e2ec7ba6eb3314c7def028e6 | MATLAB | 667 | 22 | function [AIC,SC] = LCN_calc_model_selection(N,SS,P)
% format [AIC,SC] = LCN_calc_model_selection(N,SS,P);
%
% This script will calculate criteria for model selection
% INPUT
% N = the number of samples
% P = the number of parameters in the model
% SS = the sum of squared differences between measurement and mode... |
27b25ece2f5b495796d83598d3f46503f9aa2ece92d5fbe6d1843648bdef8cc8 | MATLAB | 668 | 18 | % Local Regression and Likelihood, Figure 7.2.
%
% Conditional Hazard Rate Estimation.
% When hazard rate estimation is performed with multiple x variables,
% the result is an estimate of the conditional hazard rate for the
% first variable, given the levels of the remaining variables.
%
% The surface plot looks more d... |
d41c699e9ad5711779b19e437899ec56383ab0b7f349d4ef59955f98777f5977 | MATLAB | 668 | 25 | function my_system(command)
%like call_fsl, but without sourcing fslconf
if ismac()
ldsave = getenv('DYLD_LIBRARY_PATH');
else
ldsave = getenv('LD_LIBRARY_PATH');
end
%restore it even if we are interrupted
function cleanupFunc(ldsave)
if ismac()
setenv('DYLD_L... |
e04234752e66c92a03a1cd40749b7b30a1cb5409ae49aea2f7be5ebfe0084fd0 | MATLAB | 668 | 34 | function [] = alignAudio()
audioFolder = dir('*audio*');
if isempty(audioFolder)
error('no audio folder found');
elseif length(audioFolder)>1
error('too many folders?');
end
cd(audioFolder(1).name)
audioFiles = dir('*WAV');
audio = [];
for i=1:length(audioFiles)
[wav fs{i}]=audioread(audioFiles(i).name,'n... |
e08093ae1d6b8377724ab0efb01b43c0b49f7fe51477c86457d2886c1bc123c1 | MATLAB | 668 | 24 | %% scatterSpheres - plot scattered points as spheres
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% mail@andreashusch.de, husch.andreas@chl.lu
function graphicsHandle = scatterSpheres(points, diameter, c... |
ed74dfda48b5b264ac50436892a469604e39ce520f228ec57cfccf9718f504bb | MATLAB | 668 | 21 | function tree = set(tree,uid, parameter, value)
% XMLTREE/SET Method (set object properties)
% FORMAT tree = set(tree,uid,parameter,value)
%
% tree - XMLTree object
% uid - array (or cell) of uid's
% parameter - property name
% value - property value
%
% Set object properties given its uid and pairs par... |
c038c313167ada5367983f064e65474f14f9276d957bb955a55894ee5f51f8ed | MATLAB | 669 | 17 | opts = struct();
opts.spm_dir = 'PATH_TO_SPM12';
opts.max_runs_per_task = 1;
opts.echo_preference = [];
opts.vox = [3 3 3];
opts.skip_if_w_exists = true;
opts.write_tsv_confounds = true;
opts.verbose = true;
bids_root = 'PATH_TO_DATASET';
subj_list = {'sub-01','sub-02','sub-03','sub-04','sub-06','sub-08','su... |
cbfd79bf2a786e9656a99109372a81ae328247359df258e5346bf474558a47aa | MATLAB | 669 | 29 | function [vertex,face] = check_face_vertex(vertex,face, options)
% check_face_vertex - check that vertices and faces have the correct size
%
% [vertex,face] = check_face_vertex(vertex,face);
%
% Copyright (c) 2007 Gabriel Peyre
vertex = check_size(vertex,2,4);
face = check_size(face,3,4);
%%%%%%%%%%%%%%%%%%%%%%%... |
1df44ad3b7e966c5f063c72d56560b0a82558f5e017bee4fed71cb31fba08ad3 | MATLAB | 670 | 31 | function [ h ] = point_patch(x,y,s,c,resolution)
%point_patch Create nice looking scatter plot
%Example point_patch(0:pi/19:2*pi,sin(0:pi/19:2*pi),(1:39)/40,[0 0 1],20)
if nargin<5
resolution=10;
end
persistent circlex
persistent circley
persistent res
if isempty(res) || res~=resolution
res=resolution;
... |
34c90aa6108f102669366fdb110149c391079b7e3212ccd070f9e0c4b3e808da | MATLAB | 670 | 16 | function Labeling = GCO_GetLabeling(Handle,varargin)
% GCO_GetLabeling Retrieve the current labeling
% GCO_GetLabeling(Handle) returns a column vector of all labels.
% GCO_GetLabeling(Handle,i) returns the label of site i.
% GCO_GetLabeling(Handle,i,count) returns labels i..i+count-1
GCO_LoadLib(... |
8a33b7b237d8b8e08379e29c287f1260224e4a6544c4282fec1f4f167ee32363 | MATLAB | 670 | 16 | function y = logsumexp( varargin )
%LOGSUMEXP log(sum(exp(x))).
% LOGSUMEXP(X) = LOG_SUM_EXP(X) = LOG(SUM(EXP(X)). We have replaced this
% function with LOG_SUM_EXP to better match our function naming
% conventions. Please start using it instead.
warning( 'CVX:Renamed', [ ...
'The function "logsu... |
d5d70daeb0cb7219b74db2e7330ca4df0c1c58765e329bf96c7ec6c65f5c6f7a | MATLAB | 670 | 15 | % CVX_CLEAR Clears all active CVX data.
% CVX_CLEAR clears the current CVX model in progress. This is useful if, for
% example, you have made an error typing in your model and wish to start
% over. Typing this before entering another CVX_BEGIN again avoids the
% warning message that occurs if CVX_BEGIN ... |
0d9376bdb3fed51ab7d6151d8a7e366f254ffd250aef36256d314975b7ff532b | MATLAB | 671 | 18 | function s = char(tree)
% XMLTREE/CHAR Converter function from XMLTree to a description string
% FORMAT s = char(tree)
%
% tree - XMLTree object
% s - a description string of an XMLTree
%__________________________________________________________________________
%
% Return a string describing the XMLTree:
% ... |
56b3c7d5507f16719270669facc48b915ba942fe905717634afe2b495a7cde02 | MATLAB | 671 | 28 | function output = ntrodeGroups(ccf)
% ntrodeGroups
%
% This script takes in a CCF file and displays the information on the
% ntrode groups within the data file.
%
% ccf: Pass the CCF of interest. If no CCF is passed, the user will
% be prompted to choose a CCF file.
% DEFAULT: Will op... |
97b476169024da382ab459f138c5ff4527692910a571479cea22760254bf3c88 | MATLAB | 671 | 27 | function res=combnan(dat)
%Combines data in single array with NaNs separating original arrays if originally in cells
if iscell(dat)
%Remove empty cells
dat = dat(~cellfun(@isempty,dat));
if isempty(dat)
res = NaN;
return;
end
if ~iscellstr(dat)
if max(cellfun('size',dat,... |
f60d0945ff649f1bf275de384c63729b6751207c584a0d98652c29561a380953 | MATLAB | 671 | 25 | function epoch = FilterEpochs(epoch, mindur, minsep)
% For an Nx2 array of epoch values (time or otherwise), merges those closer
% than 'minsep' and removes those less than 'mindur'
%
% andrew 6/29/2011
% epoch = CMBHOME.Utils.Filterepoch(epoch, mindur, minsep)
[~, inds] = sort(epoch(:,1)); % sort ascending
epoch =... |
c2e3b9fe51977f31500723348084211d2cc9c34cbfcb820c4244cb875b15d75f | MATLAB | 672 | 25 | %% Figure 7 main
% Run fig7_analysis, then return here
fig7_analysis
% Params
colors = [[37,109,141];[78,167,160];[127,174,112];[223,189,104];[246,145,110]]/256;
% Contour params
contConfig.thresholds = [98 95 90];
contConfig.alpha = 0.5;
contConfig.lw = 0.9869;
contConfig.ls = {'-', '--', ':'};
% Areas to plot
areas ... |
9c13acedaf840d3e28f8598a659a8aadd4f1062d339ffdde3c867a2787566422 | MATLAB | 673 | 18 | % List of open inputs
% CAT12: Segmentation: Volumes - cfg_files
% Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
addpath(spm_dir)
nrun = 1; % enter the number of runs here
jobfile = {[script_dir '/CBIG_MMLDA_segment_job.m']};
jobs = repmat(jobfile, 1, nrun... |
53e8b6547b9020120dbcf9ded2ae35078f9c2746389a0184260ae74312b82c4e | MATLAB | 674 | 22 | function slope = calSlope(trialsECOG, fs, t, foi, windowSlope)
% fs in Hz
% window, windowSlope in ms
% slope: [nch x 1] in s^-1
T = 10e3; % ms, total pad duration
segNum = 20;
chMean = mu.calchMean(trialsECOG, "tail"); % [nch x ntime]
[cwtres, f] = mu.cwt(chMean, fs, segNum, "tPad", T / 1e3, "mode", "GPU", "outType"... |
9e882f39b6a3d12ac03e710b8e6e19c10fdf4376bc5d972d08e3f6b4bd38ed9b | MATLAB | 674 | 11 | % Chapter 5: Duality
%
% qcqp.m - Section 5.2.4: Solves a simple QCQP
% matrix_games.m - Section 5.2.5: Mixed strategies for matrix games
% matrix_games_LP.m - Section 5.2.5: Mixed strategies for matrix games (LP formulation)
% norm_approx.m - Examples 5.6,5.8: An l_p norm approximation problem
% ... |
10ed9c0bddd5f95010b7fb5b0cd353d5578a6f0944f291c653c5201b11ea20da | MATLAB | 675 | 17 | function dim = isvectord(vect)
%ISVECTORD Returns the orientation of a 1-D vector.
% ISVECTORD(VECT) is non-zero if exactly one dimension of VECT has
% length greater than 1. The return value is then the index of that
% dimension. Note that NDIMS can not be used to decide this question,
% because it r... |
117152ba226f96836a618178de5794c129e1416613145ab659e521a81ce6f2e7 | MATLAB | 675 | 19 | if ismac
compflags = '';
elseif isunix
compflags = ' COMPFLAGS=''$COMPFLAGS -static-libstdc++''';
% compflags = [' COMPFLAGS=''$COMPFLAGS -static-libstdc++''', ...
% ' -DPARALLEL_OPENMP', ...
% ' CXXFLAGS=''$CXXFLAGS -fopenmp''', ...
% ' LINKLIBS=''$LINKLIBS -... |
1dfa5990cdf2a704d918a1e6f3e1a8d417506e80f3463759062a7c2ad74780c2 | MATLAB | 676 | 23 | function updateSpatialDecaySlope(kilosortSavePath, qMetricSavePath)
% load in quality metrics
[~, qMetric] = load.loadSavedMetrics(qMetricSavePath);
% load in relevant kilosort files
[~, spikeTemplates, templateWaveforms, ~, ~, ...
~, ~] = load.loadEphysData(kilosortSavePath);
uniqueTemplates = unique(spikeTe... |
49453368a600d9626cb4fe4f20842fd88c20b3327b52b652bc0815ca725b85ae | MATLAB | 676 | 21 | function spineROI = saveSpine(roi_seed, roi, trace, im_norm, savepath, savename)
if ~isempty(roi_seed)
clear spineROI
k1 = 1;
for k = 1:size(roi_seed,1)
if ~isnan(roi_seed(k, 1))
spineROI(k1).roi_seed = roi_seed(k,:);
bw = roi(:,:,k);
spineROI(k1).spine_pixel = fi... |
5ce7a7b9cf45d3bd77ca18b325a467b1594773c54386f2c79d905311fc0ef00c | MATLAB | 676 | 32 | % SaveFet(FileName, Fet, BufSize)
%
% Saves a feature file
function SaveFeatures(FileName, Fet, BufSize);
if nargin<3 | isempty(BufSize)
BufSize = inf;
end
nFeatures = size(Fet, 2);
formatstring = '%d';
for ii=2:nFeatures
formatstring = [formatstring,'\t%d'];
end
formatstring = [formatstring,'\n'];
outputfile... |
749d2f02def4aa2806b63a34e1023dd2e29d71404084234199c2c326a3350dde | MATLAB | 676 | 21 | function P=ar1spectrum(ar1,period)
% AR1 power spectrum...
%
% power=ar1spectrum(ar1,period)
%
%
% (c) Aslak Grinsted 2002-2004
%
% -------------------------------------------------------------------------
% Copyright (C) 2002-2004, Aslak Grinsted
% This software may be used, copied, or redistributed... |
f8e4ed6f3139a5e623f50eae2c80f0c7ad7d3b9db0a1fc2d1b36f2ba17176e06 | MATLAB | 676 | 18 | function cmapVal = colormapVal(colormap, valMultiplier)
if size(colormap,1) ~= length(valMultiplier)
if size(colormap,1) == 1
colormap = repmat(colormap, length(valMultiplier),1); % create colormap from a single color
else
error('Colormap should be either a single color to create a map out of, o... |
f7ad460835c6052d1975b8bf37f0af281895490e6cdcdf1cf5920c6e453d0212 | MATLAB | 677 | 30 | % VOLTYPE determines the type of volume conduction model
%
% Use as
% [type] = voltype(vol)
% to get a string describing the type, or
% [flag] = voltype(vol, desired)
% to get a boolean value.
%
% See also COMPUTE_LEADFIELD
% Copyright (C) 2007, Robert Oostenveld
%
function [type] = voltype(vol, desired)
if isfie... |
33b1ba1394c3e04c38bf0537ae99b2193ecb1578d678793d3c2f3f752e5a2b9d | MATLAB | 678 | 23 | function head = loadHeadTetraMesh(meshMatPath)
%LOADHEADTETRAMESH Load a 5-layer head tetrahedral mesh produced upstream.
% Returns struct with fields:
% node (Nx3), ele (Mx5+) where column 5 is region id (1..5)
% Notes
% - This wraps whatever upstream saved as genmesh/node/ele into a standard form.
S = load(me... |
a2f53d6a0d709201f7cc7be8205829823c593b675a3e847f33fa7bea99ccd293 | MATLAB | 678 | 23 | function data=extractdatac(data,Fs,t)
% Extract segements of continuous data between t(1) and t(2)
% Usage: data=extractdatac(data,Fs,t)
%
% Input:
% data: continous data in the form samples x channels or a single vector
% Fs: sampling frequency
% t : time as a 2d vector [t(1) t(2)]
% Note that sampling frequency and... |
f10a5fea1fe992c105d3c586e05c975fd4f17c09adfe3e538b086fd175a3c995 | MATLAB | 678 | 18 | opts = @(outputDir) struct(...
'format','html',...
'stylesheet',fullfile(pwd,'../doc/','mxdom2mbgl-html.xsl'),...
'outputDir', fullfile(pwd,['../doc/html/' outputDir '/']));
try
cd ('../examples');
publish('red_black.m', opts('red_black'));
publish('record_alg.m', opts('record_alg'));
cnopt... |
7448693504121606736ae4c679df9a79e48f35125ce16abd94c4d5dc4234694c | MATLAB | 679 | 25 | function display(this)
% Display method for GIfTI objects
% FORMAT display(this)
% this - GIfTI object
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Guillaume Flandin
% $Id: display.m 4182 2011-02-01 12:29:09Z guillaume $
d... |
afdfa043c2a29e358f9800cbb8b1c4ddedf97509b85f622ef77ab2b43cacd372 | MATLAB | 679 | 26 | function tf=insurface(node,face,points)
%
% tf=innersurf(node,face,points)
%
% test if a set of 3D points is located inside a 3D triangular surface
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% node: node coordinates
% face: surface triangle list
% points: a set of 3D points (Nx3 array)
%
% out... |
3e262caf7fc5c7ba2c66f695aa55e909d43601e07ccc449905c685b08c8161ce | MATLAB | 680 | 16 | function struct12 = structcat(dim, struct1, struct2)
%STRUCTCAT Concatenates two structures field by field.
% STRUCT12 = STRUCTCAT(DIM, STRUCT1, STRUCT2) takes two structures with
% with identical fields and returns a new structure in which each field
% contains the concatenation of the corresponding fiel... |
7aebc0e889007d4c1e0ba20b4e31402424af7c10b03565bb50682179fbc6089d | MATLAB | 680 | 28 | function [A,sumV] = quadcof(N,NW,order)
% Helper function to calculate the nonstationary quadratic inverse matrix
% Usage: [A,sumV] = quadcof(N,NW,order)
% N (number of samples)
% NW: Time bandwidth product
% order: order (number of coefficients, upto 4NW)
%
% Outputs:
%
% A: quadratic inverse coe... |
7f97ca8e18c265518d3588ffdd9dc2affda7977579702befffc389ae23722765 | MATLAB | 680 | 28 | function r = circ_dist(x,y)
%
% r = circ_dist(alpha, beta)
% Pairwise difference x_i-y_i around the circle computed efficiently.
%
% Input:
% alpha sample of linear random variable
% beta sample of linear random variable or one single angle
%
% Output:
% r matrix with differences
%
%... |
13faf9107f2e22c920f54d438f79be393525ad3a023cb60dfa39157e3b0421ce | MATLAB | 681 | 20 | function AUC_PR = quickCV_PLSDA_PR(X, Y, C, opts)
% quickCV_PLSDA_PR Fast tuned cross-validated precision-recall AUC for PLS-DA.
%
% AUC_PR = quickCV_PLSDA_PR(X, Y, C, opts)
%
% Thin wrapper over quickCV_PLSDA_core with metric 'pr'. Note that the chance
% level for precision-recall AUC is the positive-class prev... |
702751aea7002399c5eb29d91e0785f5ab71cd695e85c8e46908a6b1c49c52a9 | MATLAB | 682 | 30 | function yred=rednoise(N,g,a);
% REDNOISE: A fast rednoise generator using filter.
%
% example: rednoise(N,g);
%
% Description: generates a rednoise series
% with zero process mean.
% note: statistical mean&variance will be different.
%
% Inputs: n - desired length of time series
% g - lag-1 autocorr... |
b6ded9cad99fc91c03a25cbdb5f5bbbe534d0aad81458171a400b33f3f9ee684 | MATLAB | 682 | 16 | %Several EEGLAB plugins (not included by default) are available to import
%specific data formats. To download these plugins use EEGLAB menu
%
%File > Manage Plugins > Manage data import plugins
%
%The FILEIO and BIOSIG toolboxes interface also allow to import in EEGLAB a wide variety
%of EEG/MEG data file formats -- i... |
2e31a6c03316455302856cfecd64a97972c07c57ae2f4e9f800ee2b472e04318 | MATLAB | 683 | 22 | function display(tree)
% XMLTREE/DISPLAY Command window display of an XMLTree
% FORMAT display(tree)
%
% tree - XMLTree object
%__________________________________________________________________________
%
% This method is called when the semicolon is not used to terminate a
% statement which returns an XMLTree... |
9ff384e39a67e41ac71ba689c9597b75139b5a66fc8b7bef7b73f393215514d6 | MATLAB | 685 | 20 | function x = subsref( x, S )
% Disciplined convex/geometric programming information for SUBSREF:
% The use of subscripts to extract elements or "slices" of any CVX
% variable is identical to their use with numeric arrays. All
% conventions are preserved, including the colon ':' and 'end'.
narginchk(... |
c0681637abc1b8cb895112fc8e7b907b6af03e4bd54d7194646b8cc43b26c16b | MATLAB | 685 | 18 | function plotconcats(flies,concat,colorrange)
% This is to just combine all data linearly through time, even if it's from
% different experimental protocols. Still need to match stimulus next to it
% but that's hard so it'll be for another day.
% example inputs:
% flies = ['oct1322_f2';'oct1422_f3';'oct1422_f4... |
d7094542f66a9c189ecbc2f4d06ff76d9c2d9b54c88d7b8111a9e85a2ee45eea | MATLAB | 685 | 19 | function mcmc_params = fit_meta_d_params()
% mcmc_params = fit_meta_d_params()
%
% Returns default mcmc_params for fit_meta_d_mcmc_group and fit_meta_d_mcmc
%
% SF 2015
mcmc_params.response_conditional = 0;
mcmc_params.estimate_dprime = 0;
mcmc_params.nchains = 3; % How Many Chains?
mcmc_params.nburnin = 1000; % How M... |
0d26f1a95bae24552fd0177c6efa67e8a47de34735ca9a93455e55634bc6a8bd | MATLAB | 686 | 27 | function x = Clip(x,m,M)
%Clip - Clip values.
%
% Clip values between specified extrema.
%
% USAGE
%
% clipped = Clip(x,min,max)
%
% x array to clip
% min minimum value
% max maximum value
% Copyright (C) 2004-2011 by Michaël Zugaro
%
% This program is free software; y... |
0e1d762454dd379fb391cbdbce92d2625181aaaffe140da760fb82744c309eb6 | MATLAB | 686 | 22 | function tracks = segmentTracks(data)
% SEGMENTTRACKS Split a tracking table (X Y Z T) into a cell array of
% individual track tables. A new track begins each time the T column
% resets to 0.
if ~istable(data) || ~ismember('T', data.Properties.VariableNames)
error('segmentTracks:invalidInput', ...
... |
34db81797d0aa6abf3658cdaf6389905642374dde402500ec35272fbd6c09ef7 | MATLAB | 686 | 20 | function PDIFF = chisquare_solve(XGUESS,P,V);
%CHISQUARE_SOLVE Internal function used by CHISQUARE_INV
%
% PDIFF=chisquare_solve(XGUESS,P,V) Given XGUESS, a percentile P,
% and degrees-of-freedom V, return the difference between
% calculated percentile and P.
% Uses GAMMAINC
%
% Written January 1998 b... |
373634c40d16f39e77c98d20add0d6448c87b8c70eff493a9d5e2b7822175244 | MATLAB | 686 | 28 | function x = tril( x, k )
% Disciplined convex/geometric programming information for TRIL:
% TRIL imposes no convexity restrictions on its arguments.
%
% Check inputs
%
if nargin < 2, k = 0; end
s = x.size_;
if length( s ) > 2,
error( 'The first argument must be 2-D.' );
elseif ~isnumeric( k ) || length(... |
92d14df7684442a5ab2d20fac7e569734906537148dbedcb2d6db0530392a879 | MATLAB | 686 | 38 | function formatSubplot(handle,varargin)
args.fs = 7;
args.xl = [];
args.yl = [];
args.box = [];
args.ax = [];
args.lim = [];
args.tt = [];
args.xt = [];
args.yt =[];
args = parseVarArgs(args,varargin{:});
set(handle,'fontsize',args.fs)
if ~isempty(args.xl)
xlabel(handle,args.xl)
end
if ~isempty(arg... |
a16455b1d86f1ff18286c779d4178f9eacfed3e303b08fdbe24b3f1f604997e8 | MATLAB | 686 | 28 | function x = triu( x, k )
% Disciplined convex/geometric programming information for TRIU:
% TRIU imposes no convexity restrictions on its arguments.
%
% Check inputs
%
if nargin < 2, k = 0; end
s = x.size_;
if length( s ) > 2,
error( 'The first argument must be 2-D.' );
elseif ~isnumeric( k ) || length(... |
abad9d03ca466f8dc3b835d0877a1eaacb1ae99b535ea172671c25efadcea391 | MATLAB | 686 | 26 | function h5_2_bin(path_to_file,output_name,precision,batch_size)
info = hdf5info(path_to_file);
dims = info.GroupHierarchy.Datasets.Dims;
T = dims(end);
if nargin < 4 || isempty(batch_size);
batch_size = T;
else
batch_size = min(batch_size,T);
end
if nargin < 3 || isempty(precision)
precision = 'uint16';
e... |
db07c9709fc25ff4c392e308f476e29e0d26cedeaf72cbe25ffc6739901cd957 | MATLAB | 686 | 18 | % Local Regression and Likelihood, Figure 7.2.
%
% Conditional Hazard Rate Estimation.
% When hazard rate estimation is performed with multiple x variables,
% the result is an estimate of the conditional hazard rate for the
% first variable, given the levels of the remaining variables.
%
% The surface plot looks... |
fff2650bc4e9e0c37d3a85b35e391731e81142aef218123bd9aa3ef8cbad4e16 | MATLAB | 686 | 27 | function z = ea_nanzscore(data, robust, dim)
% Computes zscores for input data
%
% data: row vector, column vector, or matrix
% If data is a matrix, z-scores are computed over columns by default
% or by specified dim.
% robust: if set to 'robust' as second argument, mean is computed excluding
% ... |
ab4f05a6a84af5c5e88bb2e24179d056f4d62c8716d64ac00c5dd228976f368b | MATLAB | 687 | 32 | function b = subsref(ipd,index)
% INPLACE/SUBSREF Support Matlab subscript references.
%
% This function supports subscript references just like Matlab matrices.
%
% Example:
% ipa = inplace(cumsum(ones(5,1)));
% ipa([2 4])
% ipa(3:end)
if (length(index) > 1)
error('Indexing operation not s... |
c658b3e1e5e800e9fa9c54f086ef2f7d637845f7d9a090fa2e1504033e63bc7b | MATLAB | 687 | 36 | D = dir;
numtests = 0;
results = [];
for di = 1:length(D)
f = D(di);
if f.isdir
continue;
end
[pathstr,name,ext] = fileparts(f.name);
if ~strcmp(ext,'.m')
continue
end;
if strcmp('rtest_all.m', f.name)
continue;
end
if strmatch('r... |
fe76f09736a0ac32de792ecec06b781254397b2424d9b22eda9ff9255759b76f | MATLAB | 687 | 26 | function saveasc(v,f,fname)
%
% saveasc(v,f,fname)
%
% save a surface mesh to FreeSurfer ASC mesh format
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2009/04/02
%
% input:
% v: input, surface node list, dimension (nn,3)
% f: input, surface face element list, dimension (be,3)
% fname: output fil... |
5650b9cccde3c52d6c71070549a92b0635e3fe677bb86e901e0e9b1fda695602 | MATLAB | 688 | 18 | % publish script
% run to print results to PDF file
cd('/Users/tor/Google_Drive/Wagerlab_Single_Trial_Pain_Datasets/Data/Tor_bmrk3_datashare')
scriptsdir = '/Users/tor/Google_Drive/Wagerlab_Single_Trial_Pain_Datasets/scripts/BMRK3';
addpath(scriptsdir)
% ---------------------------------------------------------------... |
e31d01a4e66af3cd2ae5f4dbc226528f1e2519393e7b8f861dc0b3eeac87b54f | MATLAB | 688 | 35 | function varargout = fname(varargin)
% Format
% For getting the value
% dat = fname(obj)
%
% For setting the value
% obj = fname(obj,dat)
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: fname.m 1143 2008-02-07 19:33:33Z spm ... |
832cef2eb6ddbc493660085ed77f18af569434a9a58baee1640f244983c2a8ae | MATLAB | 689 | 14 | function cbarax = find_colorbar(ax)
%FIND_COLORBAR Finds the colorbar associated with a given axes.
% CBARAX = FIND_COLORBAR(AX) returns the handle of the colorbar
% associated with the axes AX. If no colorbar is found, CBAR_AX will be
% empty.
%%%%% TMW's COLORBAR function creates a hidden proxy text objec... |
8b4031409d408cbe8cd0b51492cfaa47949676f3535656cc4b68199940e66eaf | MATLAB | 689 | 19 | function [samplelength, fileid] = ...
savesubtif(handles, sampledreg, RegPara, fileid, sample_maxL, samplelength)
if handles.savesubsampletif == 1
% save reg sample
sampledreg = max(single(sampledreg)-RegPara.I_min, 0);
sampledreg = uint8(min(ceil(sampledreg/(RegPara.I_max*1.5)*255),255));... |
34d57bf822a95989c9261911fc5221121920f6705a1f55bb5669c79ef86caf64 | MATLAB | 690 | 21 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% demo script for mesh generation from surface patches and bounding box
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% preparation
% user must add the path of iso2mesh to matlab path list
% addpath('../');
% us... |
7e1a811c127a98566cff377045caa0841b90e983f5343c05d1df7a1a6456d98a | MATLAB | 690 | 15 | %% Extract and Plot all NPS sub regions
% Once the CANlab second level batch prep_* sequence has been run, this
% script will identify all NPS subregions in the DAT object and then
% extract and plot those subregions one by one. Figures will automatically
% be saved in the figsavedir, which is set in a_set_up_paths_alw... |
1097dcbbf71a761914d168990ed8b33d44c83f4212d9f647c399d641123a491a | MATLAB | 691 | 22 | function frame = getframe(vr)
%FRAME=GETFRAME(VR)
% Returns the current frame that has been read in from video VR. Calling
% GETFRAME does not automatically advance the current frame so the user
% must first call NEXT, STEP, or SEEK before calling GETFRAME the
% first time. This makes it easy to write loops such ... |
1f9d2e4b11289f0a3ac95295471873f6a8c8903ffaac5e7397eaf498a10f4d7e | MATLAB | 691 | 27 | function [a,b,c,d]=getplanefrom3pt(plane)
%
% [a,b,c,d]=getplanefrom3pt(plane)
%
% define a plane equation ax+by+cz+d=0 from three 3D points
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% plane: a 3x3 matrix with each row specifying a 3D point (x,y,z)
%
% output:
% a,b,c,d: the coefficient for plan... |
53a823f1d39b8394ab3d5d3b86923950f005d80c0006eb58a40974af51ccc020 | MATLAB | 691 | 9 | function ret = str2vec(in)
%dodge all the weirdness in str2num, or replace it with something more bulletproof if needed
in(in == char(10) | in == char(13) | in == ';') = ' '; %try to prevent str2num from seeing any row separators, so that non-rectangular encodings don't cause errors
ret = str2num(in)'; %#ok... |
6dc6e2dd6cd3fa184265bbd96c155fdc6288c770a45765097a0c42d1d96f0713 | MATLAB | 692 | 32 | function [P bins] = JointDist(x,y,nbins)
%JOINTDIST
% Usage: [P bins] = JointDist(x,y,nbins)
%
%This function calculates the joint distribution of the variables x and y.
%It is simply a normalized histogram using hist3. nbins can take any form
%of bins that hist3 can take, but no other hist3 options.
%Written by Da... |
b03ea62b6d51bd815f25d047c6a921fb0504e6e5d37c2b06b0e62b512216b71c | MATLAB | 692 | 26 | function [rawFroi,nFrames,varargout] = TifROImask2rawFroi(img,roiStruct)
%process tif file if input is not an image matrix
if ischar(img) || isstring(img)
%always load channel 2 containing green channel
[img,imHeader] = readSCIMtif(img,2);
nFrames = imHeader.nFrames;
varargout{1} = round(imHeade... |
80c25ceb16c1682a434fbbcd02d26e54105ae53f09d78d0ac921a6dacf87b6a7 | MATLAB | 693 | 23 | function str = cvx_replicate_structure( str, sz )
%CVX_REPLICATE_STRUCTURE Apply matrix structure to N-D arrays.
szs = size( str );
nmat = prod( sz );
omat = ones( 1, nmat );
[ r, c, v ] = find( str );
nelm = length( r );
oelm = ones( 1, nelm );
r = r( : );
nvec = ( 0 : nmat - 1 ) * szs( 1 );
r = r( :, omat ) + n... |
81a3fe2e93213b9480e53849d471cd37627ba885a35be09465ca4febf39ee506 | MATLAB | 693 | 22 | function plotPolygonROIsCCF(dorsalMaps, allROIs, polygon)
% Plots the ROI centroids that fall within a supplied polygonal shape
% Figure
allenMapSMc(dorsalMaps, [-3.6, 0, -2, 3]) % Creates figure by itself
% Paper ready figure/axis formatting
panelwidth = 1.5;
panelheight = 2;
leftoffset = 0.5;
bottomoffset = 0.5;
fo... |
a657fcc295989232e18e7621fbb51e4c5e43de4026f90c02d3ee2bf740e7f8a6 | MATLAB | 693 | 33 | function p=getvarfrom(ws,name)
%
% p=getvarfrom(ws,name)
%
% get variable value by name from specified work-space
%
% author: Qianqian Fang, <q.fang at neu.edu>
%
% input:
% ws: name of the work-space, for example, 'base'
% name: name string of the variable
%
% output:
% p: the value of the specified variable,... |
f81e9e01c157df95ea7e2ebc9d53ae2dd292d6ac06900225b3c20d01009202b0 | MATLAB | 693 | 26 | function [nch, npoints, freq, d] = ddt(filename)
% ddt(filename) Read data from a .ddt file
%
% [nch, npoints, freq, d] = ddt(filename)
%
% INPUT:
% filename - if empty string, will use File Open dialog
%
% OUTPUT:
% nch - number of channels
% npoints - number of data points for each channel
% freq -... |
6e099c7fba35894cdabc5cb5e25887493e5728209076e11a25827ac0f57bdb37 | MATLAB | 694 | 31 | function Visible=CheckVisiblePoint3D(V,F,i,j)
Visible=true;
P1=V(i,:);
P2=V(j,:);
if(any(any(F==i,2)&any(F==j,2))), return, end
for k=1:size(F,1)
CF=F(k,:);
if(any(CF==i)||any(CF==j)), continue, end
O1=V(CF(1),:); O2=V(CF(2),:); O3=V(CF(3),:);
inter=LineTriangleIntersection(O1,O... |
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